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From: michael-at-shaffer.net
Date: Sat, 31 Mar 2007 14:13:04 -0500
Subject: [Microscopy] Image Analysis: round robin measurement

Contents Retrieved from Microscopy Listserver Archives
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hello all :o)

I hope to publish and present a paper at the "Automated Mineralogy"
conference this year (Sept 1-2, Brisbane, Oz). Part of it will be a section
on error analysis, and I would like to include examples of similar
determinations as accomplished by other individuals. That is, there is no
independent check on this type of measurement, and even I judged the quality
of my measurements visually. It is a very simple task using tools as
provided by all image analysis softwares, which involves segmentation of a
specific mineral in the presence of other minerals. I have posted an
example image here:
http://www.micro-investigations.com/rrr.htm
(It is an JPEG example only, and I haven't yet determined the appropriate
image)

This message is only intended to gauge the interest is such a project, but I
do imagine that some of you will recognize immediately the problems
associated with this image (and tens of others like it acquired over a short
period of time with an SEM), and who may also like to contribute beyond
measuring a single image. For example, my script has measured several
thousand of these images, and for this paper I would surely be interested in
input beyond sampling as many as possible individuals' visual acuity with a
single image. I still need to consult my co-author, but significant
contributions could mean adding co-authors ... minimally being acknowledged.

Thank you in advance for your interest (or criticisms) ...
Genuinely, Michael Shaffer :o)

SEM/MLA Research Coordinator
http://www.mun.ca/creait/maf/
Inco Innovation Centre
Memorial University
St. John's, Newfoundland
Canada



==============================Original Headers==============================
7, 18 -- From michael-at-shaffer.net Sat Mar 31 14:13:04 2007
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7, 18 -- From: "michael shaffer" {michael-at-shaffer.net}
7, 18 -- To: "MSA Microscopy list" {Microscopy-at-microscopy.com}
7, 18 -- Subject: Image Analysis: round robin measurement
7, 18 -- Date: Sat, 31 Mar 2007 16:40:51 -0230
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From: michael-at-shaffer.net
Date: Sat, 31 Mar 2007 14:15:53 -0500
Subject: [Microscopy] Image Analysis: round robin measurement (oops!)

Contents Retrieved from Microscopy Listserver Archives
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hello again :o)

Regarding my previous post to the list, I should have asked that you contact
me directly, except and unless you feel your reply is of general interest
...

Genuinely, Michael Shaffer :o)

SEM/MLA Research Coordinator
http://www.mun.ca/creait/maf/
Inco Innovation Centre
Memorial University
St. John's, Newfoundland
Canada



==============================Original Headers==============================
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6, 18 -- From: "michael shaffer" {michael-at-shaffer.net}
6, 18 -- To: "MSA Microscopy list" {Microscopy-at-microscopy.com}
6, 18 -- Subject: Image Analysis: round robin measurement (oops!)
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From: michael-at-shaffer.net
Date: Sun, 1 Apr 2007 05:58:13 -0500
Subject: [Microscopy] RE: Image Analysis: round robin measurement

Contents Retrieved from Microscopy Listserver Archives
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hello Paul, and thank you for your reply :o)

Your suggestion brings up an interesting point. That is, I haven't yet
created my "instructions" message that would outline what I want and in what
form, but it should surely invite other methods other than "grayscale
segmentation" as improperly suggested as the only method applicable.

Genuinely, Michael Shaffer :o)

SEM/MLA Research Coordinator
http://www.mun.ca/creait/maf/
Inco Innovation Centre
Memorial University
St. John's, Newfoundland



} -----Original Message-----
} From: Webster, Paul [mailto:PWebster-at-hei.org]
} Sent: March 31, 2007 6:29 PM
} To: michael-at-shaffer.net
} Subject: RE: [Microscopy] Image Analysis: round robin measurement
}
} Hi Micheal,
}
} It looks like you are seeking a way to get what biologists
} know as a volume density analysis. We do it very simply by
} placing cross-lattice overlays onto the iamges and then
} counting the number of points over the full structure and
} then counting points only over the strucuture of interest.
}
} Weibel first introduced the method and it has been verified
} by many people applying it to many applications. Hans
} Gundersen and Terry Mayhew have written a few reviews of the
} method. StereoInvestigator (MicroBrightField, in the US) and
} the CAST system (Olympus) have semi-automated it.
}
} It is a rapid, accurate way of estimating volume densities
} and if performed correctly gives a estimate with about a 5%
} error. At least is does seem to be that way for our
} biological samples.
}
} Regards,
}
} Paul Webster.
}
}
}
}
} -----Original Message-----
} From: michael-at-shaffer.net [mailto:michael-at-shaffer.net]
} Sent: Sat 3/31/2007 12:19 PM
} To: Webster, Paul
} Subject: [Microscopy] Image Analysis: round robin measurement
}
}
}
}
} --------------------------------------------------------------
} --------------
} The Microscopy ListServer -- CoSponsor: The Microscopy
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} --------------------------------------------------------------
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}
} hello all :o)
}
} I hope to publish and present a paper at the "Automated Mineralogy"
} conference this year (Sept 1-2, Brisbane, Oz). Part of it
} will be a section on error analysis, and I would like to
} include examples of similar determinations as accomplished by
} other individuals. That is, there is no independent check on
} this type of measurement, and even I judged the quality of my
} measurements visually. It is a very simple task using tools
} as provided by all image analysis softwares, which involves
} segmentation of a specific mineral in the presence of other
} minerals. I have posted an example image here:
} http://www.micro-investigations.com/rrr.htm
} (It is an JPEG example only, and I haven't yet determined the
} appropriate
} image)
}
} This message is only intended to gauge the interest is such a
} project, but I do imagine that some of you will recognize
} immediately the problems associated with this image (and tens
} of others like it acquired over a short period of time with
} an SEM), and who may also like to contribute beyond measuring
} a single image. For example, my script has measured several
} thousand of these images, and for this paper I would surely
} be interested in input beyond sampling as many as possible
} individuals' visual acuity with a single image. I still need
} to consult my co-author, but significant contributions could
} mean adding co-authors ... minimally being acknowledged.
}
} Thank you in advance for your interest (or criticisms) ...
} Genuinely, Michael Shaffer :o)
}
} SEM/MLA Research Coordinator
} http://www.mun.ca/creait/maf/
} Inco Innovation Centre
} Memorial University
} St. John's, Newfoundland
} Canada
}
}
}
} ==============================Original
} Headers==============================
} 7, 18 -- From michael-at-shaffer.net Sat Mar 31 14:13:04 2007 7,
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} 2007 14:13:04 -0500
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} n034.sc1.he.tucows.com (7.2.069.1) (authenticated as
} michael-at-shaffer.net)
} 7, 18 -- id 45B9475500D3B8B4 for
} Microscopy-at-microscopy.com; Sat, 31 Mar 2007 19:12:59 +0000
} 7, 18 -- From: "michael shaffer" {michael-at-shaffer.net} 7, 18
} -- To: "MSA Microscopy list" {Microscopy-at-microscopy.com} 7,
} 18 -- Subject: Image Analysis: round robin measurement 7, 18
} -- Date: Sat, 31 Mar 2007 16:40:51 -0230 7, 18 -- Message-ID:
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8, 21 -- Subject: RE: [Microscopy] Image Analysis: round robin measurement
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From: gmartens-at-interchange.ubc.ca
Date: Mon, 2 Apr 2007 10:44:32 -0500
Subject: [Microscopy] viaWWW: Analoug video time lapse

Contents Retrieved from Microscopy Listserver Archives
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Hi Barbara,

We have successfully used an analog video camera and just recorded
onto a 8 hour VHS tape. From here we digitized the VHS tape using
iMovie.

Good luck,

Garnet

--
Garnet Martens

Research Manager
BioImaging Facility
University of British Columbia
6270 University Blvd.
Vancouver, B.C.
Canada
V6T 1Z4

phone 604-822-3354

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From: TindallR-at-missouri.edu
Date: Mon, 2 Apr 2007 13:26:20 -0500
Subject: [Microscopy] Free stuff

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Dear Listers,

We have a Varian 880 high-vac ionization gauge that works fine, as far
as I know. At least it did when we pulled it off the TEM it was on.

We also have an Arkay Gas Burst timer in basically mint condition. It
was a spare for one of our nitrogen-burst processors, so I can't say for
sure that it works, but it looks like it's right out of the box.

You payeth for shipping, they belongeth to you.

Cheers,
Randy

Randy Tindall
Senior EM Specialist
Electron Microscopy Core Facility---We Do Small Well!
W125 Veterinary Medicine
University of Missouri
Columbia, MO 65211
Tel: (573) 882-8304
Fax: (573) 884-2227
Email: tindallr-at-missouri.edu
Web: http://www.emc.missouri.edu
On-line calendar:
http://biotech.rnet.missouri.edu/cgi-bin/Calcium310.pl?Op=Splash&Amount=
Week&NavType=Both&Type=TimePlan


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From: TindallR-at-missouri.edu
Date: Mon, 2 Apr 2007 13:35:11 -0500
Subject: [Microscopy] Free stuff retraction

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Sorry, all. In my urge to clean up the lab, I typed before I thought.

It happens that these items in my previous post will need to go through
our surplus property system, rather than through an informal give-away.

My apologies for any disappointments.

Randy

Randy Tindall
Senior EM Specialist
Electron Microscopy Core Facility---We Do Small Well!
W125 Veterinary Medicine
University of Missouri
Columbia, MO 65211
Tel: (573) 882-8304
Fax: (573) 884-2227
Email: tindallr-at-missouri.edu
Web: http://www.emc.missouri.edu
On-line calendar:
http://biotech.rnet.missouri.edu/cgi-bin/Calcium310.pl?Op=Splash&Amount=
Week&NavType=Both&Type=TimePlan


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From: m_bouchaour-at-yahoo.fr
Date: Tue, 3 Apr 2007 08:47:19 -0500
Subject: [Microscopy] AskAMicroscopist: GaN/LiNbO3 in SEM

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Below is the result of your feedback form (NJZFM-ultra-55). It was submitted by (m_bouchaour-at-yahoo.fr) from http://www.microscopy.com/Ask-A-Microscopist/Ask-A-Microscopist.html on Tuesday, April 3, 2007 at 04:01:39
---------------------------------------------------------------------------

Email: m_bouchaour-at-yahoo.fr
Name: mama bouchaour

Organization: university of metz

Education: Graduate College

Location: metz, france

Question: while i scanned a surface of GaN/LiNbO3 in SEM, i saw, under the layer of GaN a white and brillant zone anb below the bulk of liNbO3. Why this white region appear. GaN is a semiconductor and LiNbO3 is very resistive.

---------------------------------------------------------------------------

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From: dieter.bosshardt-at-zmk.unibe.ch
Date: Tue, 3 Apr 2007 08:51:42 -0500
Subject: [Microscopy] viaWWW: TRAP staining in thick MMA ground sections

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Email: dieter.bosshardt-at-zmk.unibe.ch
Name: Dieter Bosshardt

Organization: School of Dental Medicine, University of Berne

Title-Subject: [Filtered] TRAP staining in thick MMA ground sections

Question: We would like to do tartrate-resistant acid phosphatase (TRAP) staining to visualize osteoclasts in methylmethacrylate (MMA)-embedded tissues. Most people do TRAP staining in paraffin sections or in about 5 micron thick MMA sections. In the past, we successfully did TRAP staining in about 100 micron thick MMA (ground) sections. However, at the moment we are unable to repeat the TRAP staining in thick MMA ground sections.
Is there anyone out there who has a protocol for TRAP staining in thick MMA ground sections? We fixed the tissues in 4% formalin. Thanks a lot in advance.

Best regards,
Dieter Bosshardt

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From: kraftpiano-at-gmail.com
Date: Tue, 3 Apr 2007 19:31:13 -0500
Subject: [Microscopy] JEOL JSM-840 donation is here!

Contents Retrieved from Microscopy Listserver Archives
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Well, we received the SEM today. We got it off of the truck and into
the cafeteria, which we are using as a staging area until we can get
it into its permanent home in my lab upstairs. That's right,
upstairs.

Despite their best efforts to the contrary, the shipping company did
not damage it too much. The main table holding the chamber had
shifted off of the springs, but was still fairly stable when we
unpacked it. The main transformer in the bottom of the control
console had leaked all over, so we are dismantling the console to get
all the oil out. Most of the screws had fallen out of the column
itself, so we just marked the location and order of the sections and
took them off as we moved it into the cafeteria. I found a good
number of the screws stuck to the side of the ion pump magnet which
had been set on the bottom of the main scope unit.

The vacuum system is a disaster, though. Whoever disconnected this
SEM from service did a real hack job. The water hoses are cut, and
the vacuum system was almost entirely dismantled. All of the
compressed air/nitrogen lines were disconnected. Anybody have a good
schematic as to which valves get connected where?

So, here is the order of the project priorities:

1: Get everything upstairs. Most will be in pieces when it gets up
there, but we have documented it to no end (About 180 photos of the
unit all taken down)

2: Re-assemble the column and microscope console. This will include
re-working the entire vacuum system. There is oil in the diffusion
pumps, but I don't know how much. I'll check and see if it pumps
before trying to add more. There is a measurable amount, so I'm not
too worried. It looks clean and good. I need to get all the water
and air lines connected again. Again- if anybody has a schematic of
this system I would greatly appreciate it.

3: Open and clean out the main transformer tank. Replace the oil,
since most of it is in the bottom of the truck and control console.

4: Re-connect everything in the control console. Luckily most of the
cables are labeled well.

5: Figure out the six wires that were cut. There are six wires that
were cut between the center triangular console and wherever they went.
Luckily, though, I can see that they have different numbers of wires
within the cables, so I should be able to get a decent idea where they
go when I find the other end. Then, the six conductor wire gets
spliced back to the six conductor, etc...

6: Obtain a vacuum pump. There was no pump box for this system.

7: Test the vacuum seals. Since we are having to re-seal most of the
vacuum connections, I will run several dry runs with the vacuum
system. I don't see an indicator for the vacuum level anywhere on the
console. Is there a test point I can read the value off of?

8: Order new filaments. None were included. I think I'll add a set
of apertures to that as well.

9: Try to power it up and see what happens at low accelerating voltages.

10: Explore the microscopic world! (We hope.)

It looks as though this was at one point hooked up to a digital
acquisition system, as there are soldered on BNC connectors labeled
for horizontal, vertical, and beam control.

One final question: In the control console, there are two boxes at the
bottom most level. The one on the left (As you are looking at the
rear) is the main HV transformer tank. The one on the right looks
like it has some plug-in modules in it, and there is a hose running
from each module to the next module. Is this for cooling water or
oil? There were no connections or hoses that lead to the system or
away from it.

Thanks,

Justin A. Kraft

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From: marilyn.lemieux-at-genzyme.com
Date: Tue, 3 Apr 2007 20:13:55 -0500
Subject: [Microscopy] AskAMicroscopist: Koehler illumination

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This Question was submitted to Ask-A-Microscopist by (marilyn.lemieux-at-genzyme.com)
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Email: marilyn.lemieux-at-genzyme.com
Name: Marilyn LeMieux

Organization: Genzyme Genetics

Education: Graduate College

Location: Orange, CA, USA

Title: Koehler illumination

Question: Some books say that this must be performed on both low and high power as you focus on an object to be imaged (digital image). Others say that you only need to perform the koehler steps on High power(images are taken only on high power).
Do those who say to do it on both low, then high power, is that to 'get you in the ballpark' prior to going to high, or is this step unnecessary?

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From: tttan-at-SIMTech.a-star.edu.sg
Date: Tue, 3 Apr 2007 20:18:46 -0500
Subject: [Microscopy] RE: Electron beam simulation

Contents Retrieved from Microscopy Listserver Archives
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Hello,
 
I am trying to simulate electron beam heating in the SEM. I am sure this is not a new topic and perhaps lots of people had done some work on it. I am totally new to this area so like to check if anyone has good journals to recommend?
 
In my simulation, I input a figure for the probe current density (got from some journals), I inevitably gets melting... I am still trying to verify this.
 
Can anyone point out to me a typical figure for probe size, current and perhaps even current distribution equation for a TEM probe?
 
Thank you very much
 
Regards
TT
 


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From: nizets2-at-yahoo.com
Date: Wed, 4 Apr 2007 02:20:05 -0500
Subject: [Microscopy] Re: AskAMicroscopist: Koehler illumination

Contents Retrieved from Microscopy Listserver Archives
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Hi!

I don't understand your expression, but performing a
Koehler takes less than 1 min, so why bother about NOT
doing it at lower mag if this can help at higher mag?
If you think this does not help, why do you care? The
purpose it to focus the beam on your object, in the
condition you take the picture.
That said, if you take all your pictures are the same
(high) magnification, you probably don't need to
perform a Koehler each and every time.

Stephane


--- marilyn.lemieux-at-genzyme.com wrote:

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} Email: marilyn.lemieux-at-genzyme.com
} Name: Marilyn LeMieux
}
} Organization: Genzyme Genetics
}
} Education: Graduate College
}
} Location: Orange, CA, USA
}
} Title: Koehler illumination
}
} Question: Some books say that this must be performed
} on both low and high power as you focus on an object
} to be imaged (digital image). Others say that you
} only need to perform the koehler steps on High
} power(images are taken only on high power).
} Do those who say to do it on both low, then high
} power, is that to 'get you in the ballpark' prior to
} going to high, or is this step unnecessary?
}
}
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} ==============================Original
} Headers==============================
} 8, 11 -- From zaluzec-at-ultra5.microscopy.com Tue Apr
} 3 20:13:54 2007
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} of Ask-A-Microscopist)
} 8, 11 -- Subject: AskAMicroscopist: Koehler
} illumination
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From: keith.morris-at-ucl.ac.uk
Date: Wed, 4 Apr 2007 03:39:48 -0500
Subject: [Microscopy] AskAMicroscopist: Koehler illumination

Contents Retrieved from Microscopy Listserver Archives
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Hi Marilyn,

To quote: "The Koehler technique is recommended by all manufacturers of
modern laboratory microscopes because it can produce specimen illumination
that is uniformly bright and free from glare, thus allowing the user to
realize the microscope's full potential."

Find out more at:

http://micro.magnet.fsu.edu/primer/anatomy/kohler.html
http://www.aecom.yu.edu/aif/instructions/koehler/koehler.htm

Note that you should check Koehler illumination this every-time you change
objective on a microscope, and setting Koehler illumination is crucial if
you are using Phase Contrast (or DIC) optical contrast enhancement. So even
low power phase objectives require Koehler adjustment for good images via
transmission illumination. It is also required if you are capturing
transmission images via a camera (or they won't look that good at all).

For heavily stained sections at low magnifications you can get by without
bothering, but as Stephane points out it takes very little time to setup and
it is poor science not to check it every time you use the microscope
(particularly as you will have spent many hours preparing the specimen).
Previous users may have setup the optics incorrectly for various reasons.

Koehler illumination is irrelevant with epi-fluorescent imaging as with this
the light is backscattered into the objective, although often you will also
want a standard phase contrast or DIC transmission image as well. Koehler
illumination is essential for transmission images of unstained specimens
with limited contrast (where phase contrast or DIC optics is often also
required to enhance the specimens contrast by optical interference within
structures inside the specimen).

Poorly adjusted optics lead to very uneven illumination and the appearance
of dark shadows in the image. It will very badly affect contrast enhancement
optics (you won't get much enhancement). These problems are naturally best
avoided, particularly as setting the optics correctly is so easy. All
microscope manuals will tell you how to set up Kohler illumination with the
microscope (plus other important things like aligning illumination bulbs and
phase contrast rings). Expensive modern motorised microscopes can do much of
this automatically these days.

Regards

Keith

---------------------------
Dr Keith J Morris
Imaging Facilities Manager
Cell Biology
Institute of Ophthalmology
UCL, London EC1V 9EL




-----Original Message-----
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Sent: 04 April 2007 02:18
To: keith.morris-at-ucl.ac.uk

This Question was submitted to Ask-A-Microscopist by
(marilyn.lemieux-at-genzyme.com)
from http://microscopy.org/Ask-A-Microscopist/Ask-A-Microscopist.html on
Tuesday, April 3, 2007 at 12:33:59
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Question
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Please reply to both marilyn.lemieux-at-genzyme.com as well as to the
Microscopy Listserver
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Email: marilyn.lemieux-at-genzyme.com
Name: Marilyn LeMieux

Organization: Genzyme Genetics

Education: Graduate College

Location: Orange, CA, USA

Title: Koehler illumination

Question: Some books say that this must be performed on both low and high
power as you focus on an object to be imaged (digital image). Others say
that you only need to perform the koehler steps on High power(images are
taken only on high power).
Do those who say to do it on both low, then high power, is that to 'get you
in the ballpark' prior to going to high, or is this step unnecessary?

---------------------------------------------------------------------------

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From: rblyston-at-trinity.edu
Date: Wed, 4 Apr 2007 05:10:03 -0500
Subject: [Microscopy] AskAMicroscopist: Koehler illumination

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To all:

If you drive a car with a manual gear shift when you want to go, you
push in the clutch, put it into first gear and let out the clutch;
then you push in the clutch put it into second gear and let out the
clutch, then you push in the clutch and put it into third gear and
let out the clutch.

When you are driving a manual microscope, you click in the low power
objective, change the diaphragm and adjust the condenser; when you
want middle magnification (second gear) you change the diaphragm and
adjust the condenser; and when you want high power, etc.

I can continue to play with this analogy. I do not know why people
can accept moving the focus adjustment on a microscope but not the
condenser adjustment when magnification is changed. Perhaps these
poor souls did not do well in optics when they took college physics.

Bob Blystone


On Apr 4, 2007, at 2:21 AM, nizets2-at-yahoo.com wrote:

}
} Hi!
}
} I don't understand your expression, but performing a
} Koehler takes less than 1 min, so why bother about NOT
} doing it at lower mag if this can help at higher mag?
} If you think this does not help, why do you care? The
} purpose it to focus the beam on your object, in the
} condition you take the picture.
} That said, if you take all your pictures are the same
} (high) magnification, you probably don't need to
} perform a Koehler each and every time.
}
} Stephane
}
} }
} } Title: Koehler illumination
} }
} } Question: Some books say that this must be performed
} } on both low and high power as you focus on an object
} } to be imaged (digital image). Others say that you
} } only need to perform the koehler steps on High
} } power(images are taken only on high power).
} } Do those who say to do it on both low, then high
} } power, is that to 'get you in the ballpark' prior to
} } going to high, or is this step unnecessary?


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From: lcgould-at-med.cornell.edu
Date: Wed, 4 Apr 2007 08:02:42 -0500
Subject: [Microscopy] Re: AskAMicroscopist: Koehler illumination

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Dear Marilyn,
It is always good to "Kohler" every time you change lenses,
especially if you are going to take pictures (digital or otherwise).
"Kohlering" aligns the illumination system with the rest of the
microscope's optical axis, ensuring even illumination without odd
shadings or shadows. Once you get the hang of it, it only takes a few
seconds to do it, so it is certainly worth the effort.
Lee
--
Leona Cohen-Gould, M.S.
Sr. Staff Associate
Director, Electron Microscopy & Histology Core Facility
Manager, Optical Microscopy Core Facility
Weill-Cornell Medical College

voice (212)746-6146
fax (212)746-8175
http://www.cornellcelldevbiology.org
http://www.cornellbiochem.org

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From: lcgould-at-med.cornell.edu
Date: Wed, 4 Apr 2007 08:12:52 -0500
Subject: [Microscopy] Re: Koehler illumination

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Dear Marilyn,
It is always good to "Kohler" every time you change lenses,
especially if you are going to take pictures (digital or otherwise).
"Kohlering" aligns the illumination system with the rest of the
microscope's optical axis, ensuring even illumination without odd
shadings or shadows. Once you get the hang of it, it only takes a few
seconds to do it, so it is certainly worth the effort.
Lee
--
Leona Cohen-Gould, M.S.
Sr. Staff Associate
Director, Electron Microscopy & Histology Core Facility
Manager, Optical Microscopy Core Facility
Weill-Cornell Medical College

voice (212)746-6146
fax (212)746-8175
http://www.cornellcelldevbiology.org
http://www.cornellbiochem.org

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From: bfoster-at-mme1.com
Date: Wed, 4 Apr 2007 11:21:51 -0500
Subject: [Microscopy] AskAMicroscopist: Koehler illumination

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To Marilyn and anyone who uses light microscopy:

I can't stress strongly enough the importance of establishing Koehler
illumination for all techniques ... and I agree strongly with several
of the responses which stress how easy and quick the process is, once
you have done it a few times.

Koehler illumination establishes the "baseline" for all other
imaging. Setting aside alignment of the lamp filament (which
typically only needs to be done when the lamp is changed), it
involves the simple setting of focus and apertures for three key lens
sets: objective, condenser, and eyepieces. On most microscopes,
each of these lenses has adjustment for focus. Also, it is important
to understand the appropriate setting for the field iris (which
controls scatter and glare) and aperture iris (which controls
coherence and has a major impact on edge fidelity as well as resolution).

Unfortunately, today's schedule doesn't permit a long discussion, but
for those of you who are interested in a brief anatomny and
physiology less regarding each of the three key lenses and their
apertures... Plus a short recipe for establishing Koehler, send me an
email with KOEHLER, PLEASE in the subject and I'll try to send you a
PDF early next week, when I am back in the office. Also, there is a
detailed section in Optimizing Light Microscopy (call Ken Piel here
at MME for ordering information).

The take away message: PLEASE...take a few minutes to become
familiar with Koehler illumination and use it daily and check it
whenever you move from one mag to another or one technique to
another. Your microscopy will improve dramatically.

Best regards,
Barbara Foster, President

Microscopy/Microscopy Education
313 S Jupiter Rd, Suite 100
Allen, TX 75002
P: 972-954-8011
W: www.MicroscopyEducation.com


MME is now scheduling customized, on-site courses through July. Call
us today for details.

P. S.
Need a good general reference or light microscopy text for next
semester? Call us today to learn more about "Optimizing LIght
Microscopy". Copies still available through MME... even for
class-room lots ... and we give quantity discounts. Call Ken Piel at
(972)954-8011.



At 11:31 AM 4/4/2007, keith.morris-at-ucl.ac.uk wrote:



} ----------------------------------------------------------------------------
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From: frank.karl-at-degussa.com
Date: Wed, 4 Apr 2007 11:55:59 -0500
Subject: [Microscopy] Koehler illumination revisited

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Now, lets get one thing straight from the beginning. I use Koehler
illumination. I think Koehler illumination is the mark of the competent
microscopist. Don't use Koelhler illumination? As one of friends says
"Dude, that's just wrong!"

But in truth the only scope I have true Koehler illumination is a monocular
petrographic scope with a detached but focusable AO lamp with an iris.
This scope is my own at home in my lab. All the scope I have seem and used
in the last 20 years were missing some feature which prevented true Koehler
illumination.

Some were lacking centerable lamps, others immovable ground glass filters
while other did not have centerable objectives. Those that did had wire
filaments and not ribbon filaments.

I don't care whose brand...It seems impossible to set up true classic
Koehler illumination. (I don't even want to talk about focusable and
centerable Bertrand lens!)

That my story and I'm sticking to it

Frank


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From: larry.ackerman-at-ucsf.edu
Date: Wed, 4 Apr 2007 12:24:22 -0500
Subject: [Microscopy] histo staining voids

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This is more of a histology question than EM but is related. One of the
labs I work for has had problems processing/staining sections on glass
light microscopy slides when they use the Shandon Sequenza Coverplate
technology* in a rack on a cooling plate in a microwave. The problem is
small circular voids in the staining/labeling. This happens with both
immuno and general tissue stains and is similar to a phenomena I
occasionally see when staining semi-thin epoxy sections with toluidine
blue on a hot plate. It appears as if there is some localized boiling
resulting in a bubble of gas thus displacing the stain reagent.

My question is: have you experienced this phenomena and do you have a
solution for eliminating it?

* This is a patented plastic device that fits over a standard microscope
slide allowing specimens to be immunostained with a minimum of reagent
(~ 80 microliters).

Thanks, Larry
--
Larry Ackerman, Associate Specialist
UCSF, Dept. of Anatomy, Rm S1347
513 Parnassus Ave., Box 0452
San Francisco, CA 94143

larry.ackerman-at-ucsf.edu


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From: wesaia-at-iastate.edu
Date: Wed, 4 Apr 2007 16:01:02 -0500
Subject: [Microscopy] Digital cameras and the TEM

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This has been an interesting thread to follow. Each of the replies has brought out some valid points, but I don't know if they quite got to Frank's questions.
 
It is important to consider nanometers (or microns) per pixel. That will determine the ultimate resolution you have to work with. Of course Nyquist will tell you that you can't push things to the single-pixel dimensions - a couple of pixels is more likely your limit.
 
It is also important to remember that raw pixel count alone is meaningless. You have to consider the image formation process. The camera needs to be matched to the phosphor for optimum cost and performance. Excess pixels in the camera beyond the resolution of the phosphor will just waste money. Insufficient pixels will forego potential resolution. I am not a TEM fellow, so I don't know the specifics of the camera systems, but I would like to think that systems are fairly well matched by the designers, at least now that the costs of CCDs are coming down. I also won't address the limits of microscope resolution. It will enter into the picture at some magnification.
 
Frank's questions seemed to deal with appreciating or visualizing the resolution once the image was captured.
 
On the computer screen, much software seems to display the images, or portions thereof, at one pixel of image per one pixel of screen. Many screens are setup so that pixels are NOT terribly obvious to the eye from normal viewing distance. Therefore, it will be difficult to notice one pixel more or less to a dimension without zooming in on the image. The software will have full access to the image data and can make measurements down to the pixel level.
 
The printed image also raises visualization issues. Multiple dots are required to render a single pixel, at least for those printers (laser and many inkjets) where a dot is either there or not. A pattern of dots is needed together to represent shades. Therefore, the printed pixels per inch is practically an order of magnitude less than the dots per inch. And then there are the "truth in labeling" issues. What is the printer genuinely capable of?
Once again, the resolution of the eye comes into play. It is quoted at about 500 pixels (250 pixel pairs) per inch at 20 inches, but I don't think I would be appreciating one pixel more or less at that printed resolution. I have a hard time seeing jagginess in real-world, 1024-pixel-wide images printed at 5 inches. Zooming is necessary for me to clearly see individual pixels.
 
So it's time to get back to your original question about 3 megapixel cameras versus 1 megapixel cameras. My opinion is that you will only marginally appreciate the greater number of pixels on the screen or in a printed image. If your software maps images to the screen pixel by pixel, the image collected at a given magnification will be bigger on the screen and each pixel will represent a smaller dimension. The same software will probably print the image the same size and the question will be whether your eye will be able to appreciate the finer detail. It will offer larger prints (or more zoom) before pixel jagginess appears to the same degree.
 
For image analysis, the pixels will be finer at a given magnification (field of view). Therefore, you should be able to perform measurements on smaller features than before.
 
Warren Straszheim
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Let me float an question to the list.  What is the effect of changing a one
meg camera to a three meg camera on a TEM?

 I'm asked some fundamental questions, and I can't seem to answer them to
this person's satisfaction,  which implies I don't have a good grasp of the
question or answers.

 My immediate response is you would increase the resolution.  I can
envision the image size on the monitor changing,  but if the resolution of
the screen is lower than the captured image and if the computer/imaging
software wants to display all the image captured, will not any feature at a
specific magnification have the resolution of the monitor?   It seems the
same is true for the printer.  I can't simply expand the size of the paper
at will, so the software will either reduce the printed image magnification
or print just a smaller section of the total image.  Again, since the
printer has a fixed resolution will not the printed image resolution will
be limited by the printer's (This sounds like a Hi-Fi discussion from the
early 60's...  just change the words...) upper limit?

So why capture high resolution images?  My response is it allows you to
post process and expand the image to examine one feature and have
sufficient "stored" resolution to display the image without  empty
magnification.  This also implies (to me at least) if I want to measure
from point A to point B,  the more camera pixels I have the better I can
resolve where point A starts and point B ends which should allow me to have
better confidence in my measurements.  I believe that imaging software
works on the image in memory and not the image displayed on the screen so
size of the print or screen has little to do with data obtained. It's more
a function of the size of the captured image?

Lastly.....

If I feel the need to have at least 1000 pixels in an image feature, and
due to my camera I can only capture 500 at a magnification X, is there any
reason not to simply increase the magnification so I have a larger feature
which now occupies more pixels.  I realize I haven't increased the
resolution, but if my software need 999 pixels to "recognize"  a feature
haven't I met this requirement?

Thank in advance!
Frank (I miss film) Karl


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From: Edward.Calomeni-at-osumc.edu
Date: Wed, 4 Apr 2007 16:08:03 -0500
Subject: [Microscopy] histo staining voids

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Larry,

There may be two items happening. First is incomplete covering of the
sections by the reagents. I am assuming this is a capillary action type of
slide holder/stainer. Second is exactly what you mentioned, micro-boiling of
reagent.

Possible ways to help with the first is to add a surfactant/detergent to
reagents, i.e. triton/saponin in very dilute amounts.

Possible way to help with second is to lower the wattage of the microwave,
due multiple short times of microwaving, add more heat sinks to oven or go
back to the old tried and true method of overnight incubations at 4 degrees.

Ed


Edward P. Calomeni
Director EM Lab - Pathology
The Ohio State University
M018 Starling Loving Hall
320 W. 10th Ave.
Columbus, OH 43210
614-293-5580 (office)
614-293-8806 (lab)
edward.calomeni-at-osumc.edu
-----Original Message-----
X-from: larry.ackerman-at-ucsf.edu [mailto:larry.ackerman-at-ucsf.edu]
Sent: Wednesday, April 04, 2007 1:29 PM
To: Calomeni, Edward

This is more of a histology question than EM but is related. One of the labs
I work for has had problems processing/staining sections on glass light
microscopy slides when they use the Shandon Sequenza Coverplate
technology* in a rack on a cooling plate in a microwave. The problem is small
circular voids in the staining/labeling. This happens with both immuno and
general tissue stains and is similar to a phenomena I occasionally see when
staining semi-thin epoxy sections with toluidine blue on a hot plate. It
appears as if there is some localized boiling resulting in a bubble of gas
thus displacing the stain reagent.

My question is: have you experienced this phenomena and do you have a
solution for eliminating it?

* This is a patented plastic device that fits over a standard microscope
slide allowing specimens to be immunostained with a minimum of reagent (~ 80
microliters).

Thanks, Larry
--
Larry Ackerman, Associate Specialist
UCSF, Dept. of Anatomy, Rm S1347
513 Parnassus Ave., Box 0452
San Francisco, CA 94143

larry.ackerman-at-ucsf.edu


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From: TJJ-at-stowers-institute.org
Date: Wed, 4 Apr 2007 17:29:30 -0500
Subject: [Microscopy] histo staining voids

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Larry, we use this system and have not had this problem. However, in
another lab, in another galaxy, far, far away, our IHC lab had problems
with this. We deduced it was air bubble formation, and reduced the
concentration of detergent used in the rinse buffer. We currently use
0.05% Tween 20 and have no problems with it.

Careful application of the slides to the coverplate is also warranted!
If you wish, you can contact me off list and I'll give you our procedure
for mounting the slides.

Hope this helps!

Teri Johnson, HT(ASCP)QIHC
Managing Director Histology Facility
Stowers Institute for Medical Research
1000 E. 50th St.
Kansas City, MO 64110


-----Original Message-----
X-from: larry.ackerman-at-ucsf.edu [mailto:larry.ackerman-at-ucsf.edu]
Sent: Wednesday, April 04, 2007 12:31 PM
To: Johnson, Teri

This is more of a histology question than EM but is related. One of the
labs I work for has had problems processing/staining sections on glass
light microscopy slides when they use the Shandon Sequenza Coverplate
technology* in a rack on a cooling plate in a microwave. The problem is
small circular voids in the staining/labeling. This happens with both
immuno and general tissue stains and is similar to a phenomena I
occasionally see when staining semi-thin epoxy sections with toluidine
blue on a hot plate. It appears as if there is some localized boiling
resulting in a bubble of gas thus displacing the stain reagent.

My question is: have you experienced this phenomena and do you have a
solution for eliminating it?

* This is a patented plastic device that fits over a standard microscope

slide allowing specimens to be immunostained with a minimum of reagent
(~ 80 microliters).

Thanks, Larry
--
Larry Ackerman, Associate Specialist
UCSF, Dept. of Anatomy, Rm S1347
513 Parnassus Ave., Box 0452
San Francisco, CA 94143

larry.ackerman-at-ucsf.edu


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From: kraftpiano-at-gmail.com
Date: Wed, 4 Apr 2007 21:11:10 -0500
Subject: [Microscopy] First pictures of the JEOL restoration.

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Ok. First of all, before I get yelled at for dismantling the column
and stage of the SEM when removing it from the truck, be aware that
the entire top portion of the console had shifted so badly during
transit that the center of gravity was so far off that it was going to
tip over if I even looked at it funny. The only way I saw to get it
out of the truck without a major catastrophe was to take the column
apart. Since the vacuum system was already pretty much dismantled, I
didn't see that this would cause too much more pain.

As far as dismantling the control console goes, I did it because I had
to get the transformer oil out of it. It was very slippery, and
getting it clean was priority one. Thanks to those who informed me of
the PCBs. I was aware of that, and I am taking as much precausion as
possible, given the extent of the leakage. Again, not to fan the
fires, I know that it is in the cafeteria, but it was pretty much
contained in the control console and cleaned out before any parts were
placed in the cafeteria. The table that the transformer is sitting on
was broken and about to be thrown out anyway, so I used it so I don't
have to heft the transformer off the floor.

So, for your perusal, here are the first sets of photos to come out of
the restoration.

http://www.jkraft.net/semproject

Enjoy!

--Justin.

==============================Original Headers==============================
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From: ewing.hr-at-bruker-axs.com
Date: Thu, 5 Apr 2007 08:10:39 -0500
Subject: [Microscopy] viaWWW: Job Opportunity at Bruker AXS

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

This Question/Comment was submitted to the Microscopy Listserver
using the WWW based Form at http://microscopy.com/MLFormMail.html
---------------------------------------------------------------------------
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Email: ewing.hr-at-bruker-axs.com
Name: Ted Juzwak

Organization: Bruker AXS

Title-Subject: [Filtered] Job Opportunity at Bruker AXS

Question: Ý
Microanalysis Applications Engineer

Bruker AXS, Inc., a leading manufacturer of Analytical Instrumentation, has a job opening for an Applications Engineer in their Ewing, NJ Microanalysis lab. This division specializes in Energy Dispersive X-ray (EDX) Analysis instrumentation for electron microscopes.

The position entails customer, service, sales and marketing support.

Primary Responsibilities:
* Demonstration of the equipment at Bruker and customer sites
* Analysis of customer samples and production of clear analysis reports
* Provide technical support to existing, and potential customers via e- mail and phone
* User training in the operation of the Bruker Microanalysis System at Bruker and customer sites
* Produce and maintain appropriate materials for customer training
* Preparation of technical sales materials
* Assist field service in interpreting and resolving customer problems
* Perform other tasks as assigned by manager or supervisor.

This position involves up to 30% travel, primarily in North America.

Candidates interested in this position require a minimum of an Associates degree in a Physical Science discipline with a Bachelors degree in Chemistry, Geology or Materials Science preferred. Two years SEM/X-ray microanalysis experience, including sample preparation, is preferred.

Requirements include excellent communication skills and proficiency with Microsoft Office.

Send resume and salary requirement to:

Ted Juzwak
Bruker AXS Microanalysis, Inc.
1239 Parkway Avenue, Suite 203
Ewing, NJ 08628

ewing.hr-at-bruker-axs.com

Bruker AXS Inc. offers a competitive salary and comprehensive benefits package including health and dental insurance, Flexible Spending Account, company sponsored life and disability insurance, 401(k) plan with company matching components, and vacation and sick/personal days.


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From: ewing.hr-at-bruker-axs.com
Date: Thu, 5 Apr 2007 08:22:01 -0500
Subject: [Microscopy] viaWWW:Position Open at Bruker AXS

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

This Question/Comment was submitted to the Microscopy Listserver
using the WWW based Form at http://microscopy.com/MLFormMail.html
---------------------------------------------------------------------------
Remember this posting is most likely not from a Subscriber, so when replying
please copy both ewing.hr-at-bruker-axs.com as well as the MIcroscopy Listserver
---------------------------------------------------------------------------

Email: ewing.hr-at-bruker-axs.com
Name: Ted Juzwak

Organization: Bruker AXS

Title-Subject: [Filtered] Job Opportunity at Bruker AXS

Question: *
Microanalysis Applications Engineer

Bruker AXS, Inc., a leading manufacturer of Analytical Instrumentation, has a job opening for an Applications Engineer in their Ewing, NJ Microanalysis lab. This division specializes in Energy Dispersive X-ray (EDX) Analysis instrumentation for electron microscopes.

The position entails customer, service, sales and marketing support.

Primary Responsibilities:
* Demonstration of the equipment at Bruker and customer sites
* Analysis of customer samples and production of clear analysis reports
* Provide technical support to existing, and potential customers via e- mail and phone
* User training in the operation of the Bruker Microanalysis System at Bruker and customer sites
* Produce and maintain appropriate materials for customer training
* Preparation of technical sales materials
* Assist field service in interpreting and resolving customer problems
* Perform other tasks as assigned by manager or supervisor.

This position involves up to 30% travel, primarily in North America.

Candidates interested in this position require a minimum of an Associates degree in a Physical Science discipline with a Bachelors degree in Chemistry, Geology or Materials Science preferred. Two years SEM/X-ray microanalysis experience, including sample preparation, is preferred.

Requirements include excellent communication skills and proficiency with Microsoft Office.

Send resume and salary requirement to:

Ted Juzwak
Bruker AXS Microanalysis, Inc.
1239 Parkway Avenue, Suite 203
Ewing, NJ 08628

ewing.hr-at-bruker-axs.com

Bruker AXS Inc. offers a competitive salary and comprehensive benefits package including health and dental insurance, Flexible Spending Account, company sponsored life and disability insurance, 401(k) plan with company matching components, and vacation and sick/personal days.


---------------------------------------------------------------------------

==============================Original Headers==============================
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From: kraftpiano-at-gmail.com
Date: Thu, 5 Apr 2007 17:51:42 -0500
Subject: [Microscopy] JEOL donation- desperate cry for a part!

Contents Retrieved from Microscopy Listserver Archives
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Ok. Today we concentrated on getting the column put back together.
So far so good. We got to the point where we're doing preliminary
vacuum checks- seeing if it holds a vacuum without powering it on, but
manually actuating the valves. It doesn't. After about an hour and a
half under the column checking every gasket, we discovered a gaping
hole where there was at one point an EDS system. Ok.

We need the blanking cover for the angled opening that heads down into
the chamber! If anybody has one lying around they aren't using, I
would greatly appreciate it!

We are also missing the little thingy that one uses to place the
specimen in the chamber through the airlock. I'm staring at an open
hole, and I know that there is some kind of rod that pushes the
specimen in, but we don't have it. If there is an extra somewhere,
I'd appreciate it. If you even have one that you could photograph
closely for me so I can see if I can make one, I would appreciate that
as well.

I've posted more pictures on my site- http://www.jkraft.net/semproject

Thanks,

Justin.

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From: snelson-at-wustl.edu
Date: Thu, 5 Apr 2007 21:36:01 -0500
Subject: [Microscopy] viaWWW: Fluorescence correlation spectroscopy question

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Email: snelson-at-wustl.edu
Name: Scott Nelson

Organization: Washington University

Title-Subject: [Filtered] Fluorescence correlation spectroscopy question

Question: I use a Zeiss Confocor 2 to look at diffusion of GFP in yeast cells. My plot of G(t) sometimes contains a very strong sine wave-like oscillation with a period of about 100 hertz, and it ruins the curve. There is no obvious oscillation in the raw fluorescence intensity plot.

We guess that there is some sort of mechanical vibration in the room, but the scope is on an air table. The yeast cells are physically stuck to my slide and don't move at all. I don't see the oscillation if I look at fluorophores in solution.

Does anyone have any idea what this is and how to eliminate it?

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From: roberta.burns-at-ametek.com
Date: Thu, 5 Apr 2007 21:36:50 -0500
Subject: [Microscopy] viaWWW: JOb Opportunity at EDAX

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Email: roberta. burns-at-ametek.com
Name: Roberta Burns

Organization: EDAX

Title-Subject: [Filtered] Job Opportunity at EDAX

Question: EDAX, Inc., a leading mnaufacturer of X-Ray Microanalysis Equipment has an opening for a Technical Product Manager for TEM Products.
The position will handle all matters pertaining to EDAX elemental analysis and crystalography products for the TEM to include stategic product planning, product specification, budget/financial planning, marketing programs and sales support.

The position requires a Masters Degree in Science/Engineering and 5 years of relevant work experience.

Plesas send resumes to:
Roberta Burns
Human Resources Manager
EDAX Inc.
91 McKee Drive
Mahwah, NJ 07430



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From: steguido-at-unina.it
Date: Fri, 6 Apr 2007 08:52:36 -0500
Subject: [Microscopy] LM - Time-lapse microscopy course announcement

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html


COURSE ANNOUNCEMENT

Time-Lapse Microscopy Short Course
Live Cell Imaging for Biomedical Applications

2-4 May 2007, Villa Orlandi (Capri)

The University of Napoli “Federico II”, with the patronage of the Italian Cell
Culture Association, is organizing a time-lapse microscopy course on May 2–4,
2007 in Capri. The course is addressed to both senior scientists and students
interested in live cell imaging techniques. Both lectures and practical
sessions on video microscopy workstations will be provided.

Course organizers
Stefano Guido and Marino Simeone (University of Napoli “Federico II”, Italy)

Course overview
The recent advances in microscopy techniques, coupled with the development of
fluorescence markers, have provided scientists with an array of experimental
tools to follow processes at the cellular level in a dynamic fashion. The
purpose of this course is to provide an intensive training on state-of-the-art
methods for live cell imaging by optical microscopy, with special emphasis on
time-lapse techniques. Starting with a basic introduction to optical
microscopy, the topics covered in the course program include microscope
incubation, 3D fluorescence and multidimensional microscopy,
computer-controlled sample scanning and optical sectioning, image processing
and archiving, cell tracking, specialized fluorescence techniques (FRAP, FLIP,
FRET, SPIM, TIRFM), and time-lapse applications.

Invited speakers:
- Alberto Diaspro (Università di Genova, Italy)
- Ernst H. K. Stelzer (EMBL, Heidelberg, Germany)
- Peter Evennett (Royal Microscopical Society, UK)
- Spencer L. Shorte (Institut Pasteur, Paris, France)
- M. Cristina Cardoso (Max Delbrück Center for Molecular Medicine MDC, Berlin,
Germany)
- Roman S. Polishchuk (Consorzio Mario Negri Sud, Chieti, Italy)
- Elena V. Polishchuk (Consorzio Mario Negri Sud, Chieti, Italy)
- Tony Collins (McMaster University, Hamilton, Canada)
- Dario Parazzoli (National Institute of Molecular Genetics INGM, Milano,
Italy)

MAIN SPONSOR: Okolab, Italy (http://www.oko-lab.com)
OTHER SPONSORS (to be updated): Zeiss, Hamamatsu, Coherent, Molecular Cytomics
Official media partner: Imaging & Microscopy.

Please find more information on the course website:
http://www.time-lapse-microscopy.unina.it or send an email to
segreteria-at-time-lapse-microscopy.unina.it


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From: jmastrangelo-at-ulbi.com
Date: Fri, 6 Apr 2007 20:51:53 -0500
Subject: [Microscopy] viaWWW: SEM preparation for insects, other recommendations

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Email: jmastrangelo-at-ulbi.com
Name: Joe Mastrangelo

Organization: Ultralife Batteries

Title-Subject: [Filtered] SEM preparation for insects, other recommendations

Question: Our company typically sponsors a tour for "National Bring your Child to Work Day". Now that we have a SEM in house, I hope to be able to make their visit to our lab a memorable one.

Since most of my imaging is done on powders, mixtures, coatings, etc. I figure something a little more interesting might be in order. I would like to appeal to the listers out there for suggestions that would have relatively simple preparation techniques. My initial thoughts go to spider "face", fly eyes/legs, etc.

My questions are:

1) Any suggestions besides spider "face", fly eye/leg that would really interest the kids and might be readily available for me to find? (please include preparation techniques)

2) What type of sample preparation should I use to dehydrate insects but maintain the structures I want to image? (I would hate to have their innards all over the inside of the chamber) I seem to remember some threads talking about dehydration with methanol?

Thanks in advance for any help you can provide.

Best regards,

Joe Mastrangelo

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From: dmayes-at-carilion.com
Date: Fri, 6 Apr 2007 20:52:37 -0500
Subject: [Microscopy] viaWWW: technical TEM services for renal biopsy service

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Email: dmayes-at-carilion.com
Name: daniel mayes

Organization: carilion clinical laboratories

Title-Subject: [Filtered] technical TEM services for renal biopsy service

Question: We are a laboratory serving the Carilion Health System, a network of hospitals and healthcare facilities located mainly in southwestern Virgina, and have a renal biopsy volume requiring electron microscopy of about one per month. We are looking for a facility to perform the technical service of TEM for these renal biopsies. The interpretation of the formalin fixed material and the immunofluorescence studies are performed here. The interpretation of the electron microscopic images could be performed either by us or by the performing facility. Please contact me at dmayes-at-carilion.com, or at 540-981-7889.

Thanks.

Daniel C. Mayes, M.D.

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From: kenconverse-at-qualityimages.biz
Date: Sat, 7 Apr 2007 11:10:59 -0500
Subject: [Microscopy] viaWWW: SEM preparation for insects, other

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Joe,
My experience has been that small, hard-bodied insects like small spiders,
ants, ticks, ladybugs, even bumblebees, can just be mounted on a stub and
sputtered. In fact fresh killed, or even live insects, don't even need to
be coated until they are fully dessicated. Small spiders are particularly
tough and may just walk away after an hour or 2 under vacuum! Pieces of
leaf (especially the stoma on the bottom side) or very small flowers can be
interesting with just sputtering. The more recognizable the object on the
screen, the better the impact.

I'm assuming this is not an FESEM. I might be a little less callous about
the vacuum if it were.

If you have TV scan rate available and can find an old wind-up watch, take
the back off and watch it run.

Ken Converse
owner

QUALITY IMAGES
Servicing Scanning Electron Microscopes
Since 1981
474 So. Bridgton Rd.
Bridgton, ME 04009
207-647-4348
Fax 207-647-2688
kenconverse-at-qualityimages.biz
qualityimages.biz



-----Original Message-----
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Sent: Friday, April 06, 2007 9:56 PM
To: kenconverse-at-qualityimages.biz

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Email: jmastrangelo-at-ulbi.com
Name: Joe Mastrangelo

Organization: Ultralife Batteries

Title-Subject: [Filtered] SEM preparation for insects, other recommendations

Question: Our company typically sponsors a tour for "National Bring your
Child to Work Day". Now that we have a SEM in house, I hope to be able to
make their visit to our lab a memorable one.

Since most of my imaging is done on powders, mixtures, coatings, etc. I
figure something a little more interesting might be in order. I would like
to appeal to the listers out there for suggestions that would have
relatively simple preparation techniques. My initial thoughts go to spider
"face", fly eyes/legs, etc.

My questions are:

1) Any suggestions besides spider "face", fly eye/leg that would really
interest the kids and might be readily available for me to find? (please
include preparation techniques)

2) What type of sample preparation should I use to dehydrate insects but
maintain the structures I want to image? (I would hate to have their innards
all over the inside of the chamber) I seem to remember some threads talking
about dehydration with methanol?

Thanks in advance for any help you can provide.

Best regards,

Joe Mastrangelo

---------------------------------------------------------------------------

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==============================Original Headers==============================
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From: Mike.Bode-at-olympus-sis.com
Date: Sat, 7 Apr 2007 12:30:06 -0500
Subject: [Microscopy] viaWWW: SEM preparation for insects, other

Contents Retrieved from Microscopy Listserver Archives
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Hi Joe, this is an excellent oportunity to get kids excited about
science and microscopy. I have done this several times when I was
working as a scientist, and it's alwys fun.

I worked as a materials scientist, and we did not have any CPD
equipment, so I simply looked for dead insects in the nooks and crannies
of the lab and my home. Typically you find a good supply in corners of
the basement windows. I simply glued them to a sample holder stub (you
need to do this carefully, as they can be brittle and break. Then apply
a thin coating of gold and you have a sample that you can put in the
chamber. Put in a few. A fly, a spider, an ant, and a bug.

Perhaps a few pointers:

You can put in a sample of your powders, but the kids will most likely
not be interested in the details of grain structure or fractal
dimensions. They will lose interest quickly and become fidgety. Better
stick to flys and bugs.

Before the fun starts, put everything in your lab away that is small or
potentially dangerous. Depending on the size of the group, it is hard to
control the kids in the dark. I usually had a tape that I used to block
of an area where nobody was allowed to go, and everything that I could
not put in a cabinet was behind the tape out of reach.

The kids seemed to like to be engaged. Instead of "zooming in" on the
bug, I started out at high mag and had the kids guess at what they were
seeing. Ask them to be specific, not just "a bug". An interesting
starting point is the eye of an insect. You can zoom in between several
segments (sometimes there are hair-like structures that stick out from
there). Once you zoom out enough, the kids will identify it as a bug's
eye. The first one to give me a good answer was then allowed to "run"
the scope (change mag, and move the sample holder, slowly, of course).

Ask them what they would do if they had an SEM. Then use that to explain
some of the features. One kid, for example, told me he would use it to
watch the fish in his aquarium. Good hook to explain about vacuum, live
tissue in vacuum, why everything is black and white, etc.

Most importantly: have fun with it yourself. The kids react to your
engagement as much as they do to the pictures.

mike

Michael Bode

General Manager

OLYMPUS SOFT IMAGING SOLUTIONS CORP.
12596 West Bayaud Ave #300
Lakewood, CO 80228
USA
Tel.: +1 (303) 234-9270
Fax.: +1 (303) 234-9271
E-Mail: Mike.Bode-at-olympus-sis.net
www.olympus-sis.net

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Email: jmastrangelo-at-ulbi.com
Name: Joe Mastrangelo

Organization: Ultralife Batteries

Title-Subject: [Filtered] SEM preparation for insects, other
recommendations

Question: Our company typically sponsors a tour for "National Bring your
Child to Work Day". Now that we have a SEM in house, I hope to be able
to make their visit to our lab a memorable one.

Since most of my imaging is done on powders, mixtures, coatings, etc. I
figure something a little more interesting might be in order. I would
like to appeal to the listers out there for suggestions that would have
relatively simple preparation techniques. My initial thoughts go to
spider "face", fly eyes/legs, etc.

My questions are:

1) Any suggestions besides spider "face", fly eye/leg that would really
interest the kids and might be readily available for me to find? (please
include preparation techniques)

2) What type of sample preparation should I use to dehydrate insects but
maintain the structures I want to image? (I would hate to have their
innards all over the inside of the chamber) I seem to remember some
threads talking about dehydration with methanol?

Thanks in advance for any help you can provide.

Best regards,

Joe Mastrangelo

------------------------------------------------------------------------
---

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From: jbpawley-at-wisc.edu
Date: Sat, 7 Apr 2007 16:30:55 -0500
Subject: [Microscopy] RE: Electron beam simulation

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

--|
--|
--|Hello,
--|
--|I am trying to simulate electron beam heating in the SEM. I am sure
--|this is not a new topic and perhaps lots of people had done some
--|work on it. I am totally new to this area so like to check if anyone
--|has good journals to recommend?
--|
--|In my simulation, I input a figure for the probe current density
--|(got from some journals), I inevitably gets melting... I am still
--|trying to verify this.
--|
--|Can anyone point out to me a typical figure for probe size, current
--|and perhaps even current distribution equation for a TEM probe?
--|
--|Thank you very much
--|
--|Regards
--|TT

The current density may be high but the current itself is very low
because you have essentially a point source in the specimen.

You are right, it has been done many times. Except for really good
thermal insulators (Styrofoam?) the heating is negligible (|--1 deg C)
for beam currents of 10 to the minus 10 amps or lower. See Scanning
Electron Microscopy by Oliver Wells (1975).

Damage is usually due not to heating but to "radiation damage" cause
by the fact that most of the energy is deposited in "lumps" of more
than 20 eV each (i.e., large enough for one "lump" to break a
covalent bond). This is large and complex topic and is the reason
that it is VERY hard to make images showing better resolution than 3
nm of any covalently-bonded material (i.e., all biology). (See
Electron Crystallography on the web and authors such as Robert
Glaeser, Wah Chiu, and Ken Downing)

Cheers,

Jim Pawley

--
****************************************
Prof. James B. Pawley, Ph. 608-263-3147
Room 223, Zoology Research Building, FAX 608-262-9083
250 N. Mills St., Madison, WI, 53706 JBPAWLEY-at-WISC.EDU
"A scientist is not one who can answer questions but one who can
question answers." Theodore Schick Jr., Skeptical Enquirer, 21-2:39
"He who can get you to believe absurdities, can get you to commit atrocities."
Voltaire.

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From: raharris-at-ucdavis.edu
Date: Mon, 9 Apr 2007 11:40:12 -0500
Subject: [Microscopy] viaWWW: SEM preparation for insects, other recommendations

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

I regularly had K1-12 students tour my facility at UCD (now
deconstructed by some very stupid and unethical faculty-oops, did I say
that out loud?) Anyhow, I had a group of stubs I prepared for the kids
to view and try to guess what they were seeing. I had a stub with both
a piece of feather and a moth wing on it. I had some very small bones
and teeth from a mouse (recovered from an owl pellet). I had a
beautiful fly prep but it was much too complicated too duplicate so I
suggest a fly wing. Most people are surprised that the wing is covered
with small hairs. Flies and spiders usually collapse upon drying but
beetles, wasps, etc. will do fine with air drying. As has been noted,
many insects can be mounted live and survive the ordeal and many are
even seen to move in the vacuum though usually they are immobilized by
the expansion of the gases in their haemolymph. I would notify the
class to bring in something to look at (within reason). Had to be no
bigger than a penny, hard not soft, clean as possible. Sure, you will
get scabs and buggers but you often get something worthwhile and the
kids love that. We looked at mechanical watch parts, isopods (pill
bugs), we compared hair from different animals (all on one stub), I had
some nice cross-sections of wood, interesting leaves, insect eggs
(Lepidoptera) with micropyle visible. Another good stub is an Argentine
ant, the little tiny guys you get in your home, mounted on the same stub
as a large ant like Pogonomyrmex or better yet, Camponotus, one of the
carpenter ants. If you are careful, you can mount the tiny ant on top
of the larger ant

I made a multi-stub holder and could arrange 6 stubs at once in our
Hitachi S3500N. Always a big hit with the kids.

Rick Harris
Informational and Educational Technology (no faculty in this division!!)
University of California at Davis



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From: gary-at-gaugler.com
Date: Tue, 10 Apr 2007 21:10:49 -0500
Subject: [Microscopy] FEI Sirion SFEG upgrade

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Has anyone been through an upgrade of Sirion SFEG
(XL-30 FESEM) to de-integrate the EDAX EDS and
to upgrade the PC hardware and the OS to WinXP?

If you did, how did it go and what was the
ballpark cost? Any hidden gotchas?

tnx,
gary g.


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From: dsherman-at-purdue.edu
Date: Tue, 10 Apr 2007 21:27:09 -0500
Subject: [Microscopy] Plant microtubules

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi all,

Have any of you had success imaging higher plant microtubules? If so than I
would really appreciate the method used.

I would also appreciate a fixation protocol for microbes, yeast, or animal
microtubules that is particularly successful. This would be a starting point
if we cannot find one used on higher plants.

Although high pressure freezing and FS is an option (protocol?) I would like
to start with a chemical fixation as it would permit faster turn-around to
possibly see if the experiment is sufficiently promising to go further.

Thanks,
Debby

Debby Sherman, Director Phone: 765-494-6666
Life Science Microscopy Facility FAX: 765-494-5896
Purdue University E-mail: dsherman-at-purdue.edu
S-052 Whistler Building
170 S. University Street
West Lafayette, IN 47907
http://www.agriculture.purdue.edu/microscopy


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From: kraftpiano-at-gmail.com
Date: Wed, 11 Apr 2007 16:34:55 -0500
Subject: [Microscopy] SEM: Odds and ends from JSM-840 re-assembly.

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Ok. We've got it put together, but there are a couple of things that I'm
dwelling on. First of all, there is an ion pump but no ion pump
controller. Do I need the ion pump if I'm not running a LaB6 cathode?

Second, there are a couple of as-yet unidentified modules in the control
console. These are labeled "MSI" "STB" and "SDU." Can anyone tell me what
these modules are for? I can't make it out from following the connecting
wires.

Finally, we have an optical microscope and WDS spectrometers on the
instrument. I really don't have the ability to use these. I would love to
do some X-ray spectroscopy, however we have no controller or software to use
with these detectors.

As far as what I need now, here's the list:

1: Any sample prep equipment: Sputter coater, carbon coater, freeze dryer,
etc...

2: Any type of digital image acquisition system. We have the photographic
system, but we really can't afford the film for the number of students that
will want pictures of everything that they see. We're using this with
middle school students as well as high school students.

3: Specimen holders. Right now the stage just has the opening that goes all
the way through the rotation gear. There is no holder, and no sample
insertion rod, etc... Anything along those lines would be great.

4: Ion pump controller. (This is fairly low on the priority list, and I
would probably be willing to part with the ion pump in exchange towards
something on our wish-list.)

5: Better vacuum pump. We have a small vacuum pump that kind-of works, but
doesn't work well. I would like to get a better two-stage pump that is
actually made for SEM work, as opposed to our A/C serviceman's pump.

We have some extra items that we can sell/trade for anything you might have
extras of. First, the WDS detectors. (I can supply detailed pictures and
such if you want them) All I would ask extra for the WDS detectors are the
blanking plates- if I take them off, I'd need the plates.

I also have a Denton Desk II Carbon accessory, as well as a spare Desk II
glass cylinder for the sputter coater, (But no coater to use it with).

If we don't need the ion pump, or if we don't get a controller, I'd trade
that too.

Also, if anybody has broken unusable parts in the line of detectors and
such (I have a broken PMT) that they would be willing to part with, I would
love to have some disassembled stuff to demonstrate the different parts of
the SEM. For instance, I would love to cut a diffusion pump in half to show
how that works and make the connection to how much more of a vacuum is
needed than say, their vacuum cleaner at home.

And finally, I would like to take a moment to thank everyone on this
list for their insightful and helpful comments, as well as your
support of this project over the last couple of
weeks. I really could not have done any of this without the wonderful
advice and well-wishes from the members of this group.


--Justin A. Kraft

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From: petrov-at-mrl.uiuc.edu
Date: Wed, 11 Apr 2007 17:06:03 -0500
Subject: [Microscopy] In-Situ Electron Microscopy at AVS54

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html


Dear colleagues,

This is to inform you and to encourage you to consider participating in
the topical conference on In-Situ Electron Microscopy organized within
the 54th AVS international symposium
(http://www2.avs.org/call/2007/main.html) October 14-19, 2007, Seattle.

The topical conference call for papers is at

http://www2.avs.org/call/2007/ie.html

AVS provides a unique opportunity of electron microscopists to interact
with a wide circle of scientists who study the dynamics of materials by
in-situ techniques.

The confirmed invited speakers are:

U. Dahmen, Lawrence Berkeley National Laboratory
J.M. Howe, University of Virginia
B. Kabius, Argonne National Laboratory
I. Robertson, University of Illinois, Urbana-Champaign
R. Sharma, Arizona State University
E. Stach, Purdue University
S. Takeda, Osaka University, Japan, "In-situ Environmental TEM of the
Nucleation and Growth of One-Dimensional Nanostructures"
J.M. Zuo, University of Illinois, Urbana-Champaign

If you have suggestion for names of other invited speakers please
contact the topical conference organizers:

Suneel Kodambaka (kodambaka-at-ucla.edu)
Ivan Petrov (petrov-at-uiuc.edu)





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From: nholson-at-ucsd.edu
Date: Wed, 11 Apr 2007 19:15:25 -0500
Subject: [Microscopy] Postdoc or JR Staff position at UC San Diego

Contents Retrieved from Microscopy Listserver Archives
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--
A postdoctoral or junior staff position, with demonstrated experience
in electron cryo-microscopy, is open in the laboratory of Dr. Timothy
S. Baker at the University of California - San Diego in the Chemistry
and Biochemistry Department.

Applications will be accepted from individuals who possess a degree
in the Natural Sciences (Ph. D. for postdoctoral position only). The
salary and level of the position will be commensurate with the
candidate's experience and skills.

The research focuses on structure-function studies of macromolecular
assemblies (primarily viruses) with cryo-TEM and 3D image
reconstruction techniques. Highly-motivated candidates with
significant experience in cryo-TEM and/or cryo-tomography, along with
experience in image reconstruction and molecular image analysis, are
encouraged to apply. See http://cryoem.ucsd.edu/facilities.shtm for
a description of facilities. Image processing is performed in-house
on a three-node Linux cluster housed at the San Diego Supercomputer
Center, an organized research unit of UCSD. Additional computations
are performed using the NSF supported TeraGrid resources.

San Diego is a vibrant, cosmopolitan city, known for its beautiful,
year-round climate. The area includes about 70 miles of beaches, and
water sports such as surfing, snorkeling, kayaking and fishing are
all very popular. Winter alpine skiing and the deserts are within a
couple of hours drive. The city is home to both the San Diego
Chargers and the San Diego Padres. Mexico is close enough for an
afternoon trip.

Qualified applicants should send a CV that identifies areas of
expertise and interest, employment history, a publications list, and
the names and contact information of three, professional references
to Dr. Timothy S. Baker, Professor of Chemistry/Biochemistry _and
Molecular Biology, _University of California, San Diego_, 9500 Gilman
Drive MC-0378, La Jolla, California 92093-0378. Alternatively, CVs
may be sent to tsb-at-ucsd.edu. See http://cryoem.ucsd.edu for more
information about the laboratory.

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From: gstrout-at-ou.edu
Date: Thu, 12 Apr 2007 12:05:47 -0500
Subject: [Microscopy] Reichert Ultracut motor drive belt

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

I have a Reichert Ultracut that is badly in need of a new motor drive
belt. I have changed these belts on other microtomes, but not an
Ultracut. It is not immediately obvious how the belt comes off the
pully located behind the flywheel/handcrank. Does anyone have
instructions for changing out this belt?

Who is the current technical representative for the older Reichert
machines and does Leica Microsystems currently hold the Reichert name?

Thanks,
Greg

--
--
==================================================================
Greg Strout
Electron Microscopist, University of Oklahoma
WWW Virtual Library for Microscopy:
http://www.ou.edu/research/electron/www-vl/
e-mail: gstrout-at-ou.edu
Opinions expressed herein are mine and not necessarily those of
the University of Oklahoma
==================================================================



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From: mraderma-at-physiology.med.uvm.edu
Date: Thu, 12 Apr 2007 13:36:43 -0500
Subject: [Microscopy] 3rd UVM course on 3D reconstruction of single particles

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Dear all,

We are happy to announce the

3rd UVM Practical Course
on Three-dimensional Cryo Electron Microscopy of Single Particles
August 13-19 2007,
University of Vermont, Burlington, VT


This international course will teach the principles of three-dimensional
reconstruction of single particles from cryo electron micrographs. The course
will include a lecture series teaching in-depth the basic theoretical principles
of single particle analysis and discussions and demonstrations of experimental
procedures. Six hours per day are allocated for hands-on processing of data sets
from electron micrographs of single particles.

Participants will work in groups of two. Each group will have one instructor,
who will provide step-by-step guidance through the complete three-dimensional
reconstruction process and offer additional explanations and support. The course
aims to provide participants with a strong practical and theoretical background
that will enable them later to use these techniques in their home laboratory.

For details please visit:

http://physioweb.med.uvm.edu/Cryo_Practical/


______________________________________________
Michael Radermacher, Assoc. Prof.
University of Vermont
Dept. Molecular Physiology and Biophysics
HSRF 120 / 149 Beaumont Ave
Burlington, VT 05405






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From: wcrgs-at-aol.com
Date: Fri, 13 Apr 2007 08:12:50 -0500
Subject: [Microscopy] viaWWW: Potential difference across a microscope slide

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

This Question/Comment was submitted to the Microscopy Listserver
using the WWW based Form at http://www.microscopy.com/MLFormMail.html
---------------------------------------------------------------------------
Remember this posting is most likely not from a Subscriber, so when replying
please copy both wcrgs-at-aol.com as well as the MIcroscopy Listserver
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Email: wcrgs-at-aol.com
Name: Ronald Obie

Organization: WCRG

Title-Subject: [Filtered] Potential difference across a microscope slide

Question: Hello.
Does anyone know of a microscope slide available which has the capability for a potential difference to be placed across it? We would like to evaluate the charge of various particles by looking at the direction to which they move relative to the charge placed at the edge of a cover slip. Has anyone ever tried this? Are there references available?
Thank you for your response.
Ronald Obie
WCRG
336-841-0264


---------------------------------------------------------------------------

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From: cervantes-at-bendres.com
Date: Fri, 13 Apr 2007 14:55:46 -0500
Subject: [Microscopy] Reference for EM of Biological Tissues and Cells

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Can anyone recommend a good reference for electron microscopy images of
biological tissues and cells? I have Bozzola's Electron Microscopy:
Principles and Techniques for Biologists, but would like a reference
focused on identification of tissues/cells, rather than technique.
Thanks and TGIF,
Jessica Cervantes
Bend Research, Inc
Bend, OR



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From: cervantes-at-bendres.com
Date: Fri, 13 Apr 2007 15:12:47 -0500
Subject: [Microscopy] TEM: Alternative to Uranyl Acetate Stain

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Due to some bureaucratic mumbo-jumbo, I am not able to use Uranyl
Acetate (nuclear warheads, blah, blah, blah). I would like to stain
some osmium-fixed tissue thin-sections for TEM; the procedure I'm
following has a UA/Sato's lead stain step for the sections. Does anyone
know of a suitable alternative? I did a quick google and listserver
archive search and didn't find anything, but I'm hoping someone has run
into this problem before and can suggest something.

Crossing my fingers,
Jessica Cervantes
Bend Research, Inc
Bend, OR


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From: lcgould-at-med.cornell.edu
Date: Fri, 13 Apr 2007 15:19:28 -0500
Subject: [Microscopy] Re: Reference for EM of Biological Tissues and Cells

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Dear Jessica,
If you can find it, you can't do much better than HISTOLOGY: A Text
and Atlas by Johannes AG Rhodin. The copy I have is copyrighted
1974. It was published by Oxford University Press.
Lee
--
Leona Cohen-Gould, M.S.
Sr. Staff Associate
Director, Electron Microscopy & Histology Core Facility
Manager, Optical Microscopy Core Facility
Weill-Cornell Medical College

voice (212)746-6146
fax (212)746-8175
http://www.cornellcelldevbiology.org
http://www.cornellbiochem.org

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From: Walter.Bobrowski-at-pfizer.com
Date: Fri, 13 Apr 2007 15:33:18 -0500
Subject: [Microscopy] Re: Reference for EM of Biological Tissues and

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Histology: A text and Atlas was updated 2006 (paperback) with CD-ROM and
is available from Barnes & Noble.
Another excellent choice is Color Atlas of Cytology, Histology and
Microscopic Anatomy by Wolfgang Kuehnel, also available from B&N. The
paperback edition is excellent!

Best regards,

Walter F. Bobrowski
Sr. Scientist
Pfizer Global R&D
2800 Plymouth Rd.
Ann Arbor, MI 48105

TEL: 734-622-7814
FAX: 734-622-5718

"Like the strength of a steel rod, the true character of a person can
only be known under extreme stress." - Leslie Fieger




-----Original Message-----
X-from: lcgould-at-med.cornell.edu [mailto:lcgould-at-med.cornell.edu]
Sent: Friday, April 13, 2007 4:24 PM
To: Bobrowski, Walter

Dear Jessica,
If you can find it, you can't do much better than HISTOLOGY: A Text
and Atlas by Johannes AG Rhodin. The copy I have is copyrighted
1974. It was published by Oxford University Press.
Lee
--
Leona Cohen-Gould, M.S.
Sr. Staff Associate
Director, Electron Microscopy & Histology Core Facility
Manager, Optical Microscopy Core Facility
Weill-Cornell Medical College

voice (212)746-6146
fax (212)746-8175
http://www.cornellcelldevbiology.org
http://www.cornellbiochem.org

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From: neerajg-at-clemson.edu
Date: Sat, 14 Apr 2007 15:51:38 -0500
Subject: [Microscopy] viaWWW: Animations for Tomography

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Email: neerajg-at-clemson.edu
Name: Neeraj V. Gohad

Organization: Clemson University

Title-Subject: [Filtered] Animations for Tomography

Question: Dear all,

I will be giving a seminar on Electron Tomography in our department as a part of our departmental seminar series. I am searching for animations illustrating the process of tomography, I do have schematics and animations showing the weighted backprojections and aligned stacks. I am looking for an animations which shows the electrons hitting the specimen in the column as the tilt series is being taken. Does any one know a source where I can find an animation and or schematic?

As always I appreciate everyoneís help ,

Regards,

Raj.

Neeraj V. Gohad
Graduate Research Assistant
Department of Biological Sciences
Clemson University,
Clemson, SC-29634



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From: phillipst-at-missouri.edu
Date: Sat, 14 Apr 2007 21:04:03 -0500
Subject: [Microscopy] Re: Reference for EM of Biological Tissues and

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Don Fawcett's The Cell (publisher = Saunders) has superb TEM views of most
organelles. don't know if it is still in print.

At 02:57 PM 04/13/07, you wrote:



} ----------------------------------------------------------------------------
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Thomas E. Phillips, PhD
Professor of Biological Sciences
Director, Molecular Cytology Core
2 Tucker Hall
University of Missouri
Columbia, MO 65211-7400

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573-882-0123 (fax)
PhillipsT-at-missouri.edu
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From: sally.stowe-at-anu.edu.au
Date: Sun, 15 Apr 2007 18:25:39 -0500
Subject: [Microscopy] RE: Reichert Ultracut motor drive belt

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Does anyone have a service manual for Ultracuts and /or Ultracut Es ?

Thanks
Sally


Dr SJ Stowe
Facility Coordinator
ANU Electron Microscopy Unit
ANU CRICOS#00120C



} -----Original Message-----
} From: gstrout-at-ou.edu [mailto:gstrout-at-ou.edu]
} Sent: Friday, 13 April 2007 3:06 AM
} To: sally.stowe-at-anu.edu.au
} Subject: [Microscopy] Reichert Ultracut motor drive belt
}
}
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From: cgarber-at-2spi.com
Date: Sun, 15 Apr 2007 22:25:09 -0500
Subject: [Microscopy] Special microscope slide request

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Ronald Obie wrote:
==============================================================
Does anyone know of a microscope slide available which has the capability
for a potential difference to be placed across it? We would like to
evaluate the charge of various particles by looking at the direction to
which they move relative to the charge placed at the edge of a cover slip.
Has anyone ever tried this? Are there references available?
=======================================================
We at SPI Supplies have offered a line of ITO (indium tin oxide) coated
microscope slides, see URL
http://www.2spi.com/catalog/standards/ITO-coated-slides-resistivities.html

If you want microscope slide sizes substrates, then at the bottom, click on
"Microscopy Slides". They are also available with busbars which makes for
an easier connection for electrical contacts. The slides are available at
different resistivities.

Note that we also offer ITO coated cover slips, either with or without
busbars.

Chuck

===================================================
Charles A. Garber, Ph. D. Ph: 1-(610)-436-5400
President
SPI SUPPLIES FAX: 1-(610)-436-5755
PO BOX 656 e-mail: cgarber-at-2spi.com
West Chester, PA 19381-0656 USA Cust. Service: spi2spi-at-2spi.com


Look for us!
############################
WWW: http://www.2spi.com
############################
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From: rcmoretz-at-gmail.com
Date: Mon, 16 Apr 2007 07:22:27 -0500
Subject: [Microscopy] Re: TEM: Alternative to Uranyl Acetate Stain

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Jessica:

You can get depleted (or at least you used to be able to get this) UAc
so that your safety people (or whoever) can be assured that you are
not getting into making nuclear warheads, etc. Of course, I suppose
that trying to reason with them by noting the very small amount you
would be receiving could not be used for such purposes, plus it is not
enriched U but natural isotopes.... Probably too much to hope that
reason and logic has any place in such discussions.

Roger Moretz, Ph.D.
Dept. of Toxicology
Boehringer Ingelheim Pharmaceuticals, Inc.

Disclaimer: The comments and opinions are those of the author alone,
and do not reflect any official position by his employer.

On 4/13/07, cervantes-at-bendres.com {cervantes-at-bendres.com} wrote:
}
}
}
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}
} Due to some bureaucratic mumbo-jumbo, I am not able to use Uranyl
} Acetate (nuclear warheads, blah, blah, blah). I would like to stain
} some osmium-fixed tissue thin-sections for TEM; the procedure I'm
} following has a UA/Sato's lead stain step for the sections. Does anyone
} know of a suitable alternative? I did a quick google and listserver
} archive search and didn't find anything, but I'm hoping someone has run
} into this problem before and can suggest something.
}
} Crossing my fingers,
} Jessica Cervantes
} Bend Research, Inc
} Bend, OR
}
}
} ==============================Original Headers==============================
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From: carnahan-at-edison-labs.com
Date: Mon, 16 Apr 2007 07:58:52 -0500
Subject: [Microscopy] RE: Potential difference across microscope slide.

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Ronald,



We prepare slides for micro-electrochemistry from standard 1X3 glass slides
which are masked with a strip of tape over the region that will hold the
sample then sputter coated with gold using 3-5X the exposure used for SEM
sample prep. Be sure to wrap the tape all the way around the slide and also
along the back to avoid conductive paths along the edges and to avoid
conduction paths to the stage. We typically use tape cut to 3mm for our
cell width and also mask the entire back and edges of the slide. After
sputtering, we clean the slide and use a drop of conductive silver paint (
the usual SEM suppliers) to attach flexible lead wires. The samples are
applied and covered with a square cover slip.



Our own applications are all low voltage but if you intend to run at high
voltages you need to prepare very carefully for microscopist safety. If you
are intending to use high voltages, especially electrophoresis supplies, you
need to get competent design and audit help from electrical engineers with
high voltage safety experience.



James Carnahan

Edison Analytical Laboratories, Inc.
301 Nott Street
Schenectady, NY 12305

(518) 393-2112



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From: cervantes-at-bendres.com
Date: Mon, 16 Apr 2007 10:57:44 -0500
Subject: [Microscopy] TEM:Alternative to Uranyl Acetate Stain

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Thanks to everyone who responded. I have indeed brought up the fact
that the UA is from depleted uranium, and will continue to try to reason
with people. I have managed to get sodium cacodylate (it contains
arsenic!) and OsO4 (can blacken your eyeball!) in the door, so there is
some hope . . . in the meantime at least now I have some alternatives to
try.

Thanks again.

Jessica Cervantes
Bend Research, Inc
Bend, OR



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From: cervantes-at-bendres.com
Date: Mon, 16 Apr 2007 10:58:04 -0500
Subject: [Microscopy] Re: Reference for EM of Biological Tissues and Cells

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Thanks to everyone who provided references. I've got quite the list now
. . .

Jessica Cervantes
Bend Research Inc
Bend, OR


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From: tbargar-at-unmc.edu
Date: Mon, 16 Apr 2007 10:58:42 -0500
Subject: [Microscopy] cell cultures and aldehyde fixatives

Contents Retrieved from Microscopy Listserver Archives
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Dear listers,

I'm processing some monolayer cell cultures grown on Thermanox coverslips
for SEM. I seem to recall that aldehyde fixatives can cause an artifact
that results in small holes in the cell membrane. If I remember, Picric
Acid is added to the fixative and that it helps prevent the artifact. I
don't remember where I originally read this. Am I off base on this? If it
is correct, does anyone out there remember the formulation of the fixative
using Picric Acid? I currently use 2% glutaraldehyde, 2% paraformaldehyde
and 0.5% acrolein in 0.1M Sorensen's phosphate buffer 7.2pH.

Also during processing the thin cytoplasmic extensions of the cells break.
I assume this is due to shrinkage during the dehydration steps and critical
point drying. Anyone know of a way to prevent this?

All help is appreciated. Thanks.

Tom Bargar
University of Nebraska Medical Center
Core Electron Microscopy Research Facility
986395 Nebraska Medical Center
Omaha, NE 68198-6395
402-559-7347
tbargar-at-unmc.edu


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From: oshel1pe-at-cmich.edu
Date: Mon, 16 Apr 2007 11:44:18 -0500
Subject: [Microscopy] Re: cell cultures and aldehyde fixatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Tom,

For the membrane holes, try 1% tannic acid in the glut. You want the
monomeric form, Mallinckrodt 1674 - or 1764, I keep transposing those
digits. 1% T.A. can also be used in an OsO4 post-fix.
I would also suggest cutting the glut to 1 or 1.25%, and don't bother
with the formalin, it's not neeed for cell monolayers.
Acrolein I haven't used, so can't comment. I've just done 1-1.25%
glut + 1% tannic acid.
I don't know about picric acid, and would be interested to hear if it works.

Phil

} Dear listers,
}
} I'm processing some monolayer cell cultures grown on Thermanox coverslips
} for SEM. I seem to recall that aldehyde fixatives can cause an artifact
} that results in small holes in the cell membrane. If I remember, Picric
} Acid is added to the fixative and that it helps prevent the artifact. I
} don't remember where I originally read this. Am I off base on this? If it
} is correct, does anyone out there remember the formulation of the fixative
} using Picric Acid? I currently use 2% glutaraldehyde, 2% paraformaldehyde
} and 0.5% acrolein in 0.1M Sorensen's phosphate buffer 7.2pH.
}
} Also during processing the thin cytoplasmic extensions of the cells break.
} I assume this is due to shrinkage during the dehydration steps and critical
} point drying. Anyone know of a way to prevent this?
}
} All help is appreciated. Thanks.
}
} Tom Bargar
} University of Nebraska Medical Center
} Core Electron Microscopy Research Facility
} 986395 Nebraska Medical Center
} Omaha, NE 68198-6395
} 402-559-7347
} tbargar-at-unmc.edu
--
Philip Oshel
Microscopy Facility Supervisor
Biology Department
024C Brooks Hall
Central Michigan University
Mt. Pleasant, MI 48859
voice: (989) 774-3576
dept. fax: (989) 774-3462

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From: lcgould-at-med.cornell.edu
Date: Mon, 16 Apr 2007 11:54:22 -0500
Subject: [Microscopy] Re: cell cultures and aldehyde fixatives

Contents Retrieved from Microscopy Listserver Archives
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HI Tom-
I use picric acid in my primary fix to preserve membranes. My
"recipe" is 2.5% glut, 4% pfa in 0.1M Na-cacod. with 0.02% picric
acid. I did the math years ago, and this worked out to be:
1 vial of 10% glut + 1 vail of 16% pfa in 20 ml of 0.2m cacod with 2
ml of saturated aqueous picric acid added.
I've had the same 100g bottle of picric acid for over 15 years. I
just keep it saturated with the liquid well above the level of the
crystals. When I draw some off, I add more water. Our Life Safety
guys here are just thrilled with me: osmium, uranium picric acid,
suspected carcinogens ...all the fun stuff we EM folk play with. As
long as you are careful about keeping the crystals fully under water,
and not letting any accumulate around the rim or anywhere where they
could dry out, you're fine.

As for your broken processes: they may be getting beaten up during
your CPD run. Be sure to do your CO2 exchanges gently, never letting
the fluid level drop below your sample (this will mean extra
exchanges), and then, at the end, vent very slowly...100 psi/minute
or less.

Good luck!
Lee
--
Leona Cohen-Gould, M.S.
Sr. Staff Associate
Director, Electron Microscopy & Histology Core Facility
Manager, Optical Microscopy Core Facility
Weill-Cornell Medical College

voice (212)746-6146
fax (212)746-8175
http://www.cornellcelldevbiology.org
http://www.cornellbiochem.org

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From: drk-at-SHCC.org
Date: Mon, 16 Apr 2007 12:05:52 -0500
Subject: [Microscopy] fixation of lysosome membranes

Contents Retrieved from Microscopy Listserver Archives
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Greetings Microscopists,

We are trying to stabilize lysosomes for section surface immunocytochemisty
and are searching for a fixation method which might best preserve the
membranes without destroying antigenicity. We are working with cultured
cells embedded in LR White. Our usual method of 4% paraformaldehyde with
1.0% glut (buffered with culture media) appears to allow stabilization thru
approximately 70% EtOH, but the lysosomes appear to break afterwards,
spilling their contents into the cytoplasm. Fixation and dehydration were
done on ice. We are considering a PLT procedure, perhaps also including a
little Uranyl acetate in the fixative. Are there any suggestions for
preserving these delicate membranes?

Many thanks,

Doug

Douglas R. Keene
Assistant Investigator
Micro-Imaging Center
Shriners Hospital for Children
3102 S.W. Sam Jackson Park Road
Portland, Oregon 97239
503-221-3434
drk-at-shcc.org



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From: cervantes-at-bendres.com
Date: Mon, 16 Apr 2007 12:57:05 -0500
Subject: [Microscopy] TEM:Alternatives to Uranyl Acetate Stain - Responses to the Original Query

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

A couple of you have asked what the responses were to my query for
alternatives to UA. Here's the list:

1. Bismuth Staining - from Mike Nesson

Quote: There are several references that deal with Bismuth staining. I
tried some of these years ago and was quite satisfied with the results.

Locke, M and Huie, P. "Bismuth staining for light and electron
microscopy" Tissue and Cell: 9; 347-371 (1977).


2. Straight lead citrate - from Ted, Managing Director, The EMscope
Company Ltd., Thailand.


3. Nanovan (a negative stain)- from David Gene Morgan, University of
California at Davis

Quote: There is a product called nanovan (sold by Nanoprobes) which is a
methylamine vanadate stain that has similar features to uranly acetate.
The manufacturers claim finer grain size and some other benefits, if I
remember correctly. The only uses I am aware of have been to replace
simple uranyl acetate staining of isolated biological materials, and I
have no idea if it would even work as a TEM post-stain.


4. Reduced Osmium - from Rachid

Quote: There is no need for UA if your sample is treated with reduced
osmium (osmium + potassium ferrocyanide). You will just have to
contrast 2 min with lead citrate ... the contrast you will get will be
really good. You can check on this web site that I am putting together
... all pictures in the gallery are produced as I mentioned.
http://rsougrat.googlepages.com/


5. KMnO4 and/or Tannic Acid - from Mike Reedy

Quote: You will get even more contrast if you use KMnO4 followed by
Sato's, as we have since 1964 (when Pb was was Pb cittrate, not Sato's).
And, you can get good contrast on thinner sections. Using Tannic acid
in the block stain, before OSO4, or after but followed by UrAc, adds to
contrast, improves preservation. We have had excellent results (see
attached).

Some reports of using TA as a section stain before Pb stain can also be
found with google help. I've never tried it yet.

KMnO4 section stain won't work if NMA is in your Epon mix. End quote.

Mike included attachments in his reply, which can't be posted.


6. Tell the safety people to get a brain - from several people


Thanks again to everybody who responded. This is a great resource.

Jessica Cervantes
Bend Research Inc
Bend, OR



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From: lcgould-at-med.cornell.edu
Date: Mon, 16 Apr 2007 15:46:45 -0500
Subject: [Microscopy] cell cultures and aldehyde fixatives

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In 1964, I published a small note about the potential use of Indium
Trichloride as a stain during embedding (J de Microscopie, 3: pp575-
578). As I recall, it added some contrast, specifically to virus
structures. It might be worth considering.

Joel

Date sent: Mon, 16 Apr 2007 12:57:11 -0500
To: jbs-at-temple.edu
X-from: cervantes-at-bendres.com
Send reply to: cervantes-at-bendres.com


Hi All,
Jan Leunissen pointed out that I neglected to include the original
volumes of the vials of pfa and glut...sorry about that. I buy 10ml
vials of both.
Lee
--
Leona Cohen-Gould, M.S.
Sr. Staff Associate
Director, Electron Microscopy & Histology Core Facility
Manager, Optical Microscopy Core Facility
Weill-Cornell Medical College

voice (212)746-6146
fax (212)746-8175
http://www.cornellcelldevbiology.org
http://www.cornellbiochem.org

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From: rpowell-at-nanoprobes.com
Date: Mon, 16 Apr 2007 18:21:33 -0500
Subject: [Microscopy] viaWWW: TEM:Alternatives to Uranyl Acetate Stain

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Email: rpowell-at-nanoprobes.com
Name: Rick Powell

Organization: Nanoprobes, Incorporated

Title-Subject: [Microscopy] TEM:Alternatives to Uranyl Acetate Stain

Question: Response from commercial vendor (Nanoprobes):

Hello Everyone:

We do offer "NanoVan" as a commercial product. It is based on methylamine vanadate, which has a lower atomic number than uranium, and will give a ligher stain (since we make small gold particles, this is helpful).

We also offer Nano-W, an alternative based on tungsten which produces a denser stain. The two may be combined for intermiediate stain densities.

Catalog and information:

http://www.nanoprobes.com/Nstain.html

Newsletter article:

http://www.nanoprobes.com/Vol8_Iss3.html#4

Hope this is helpful,

Rick Powell

Nanoprobes, Incorporated
www.nanoprobes.com

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From: DLowry-at-asu.edu
Date: Mon, 16 Apr 2007 18:21:56 -0500
Subject: [Microscopy] viaWWW: Mycobacterium prep for immuno-label

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Email: DLowry-at-asu.edu
Name: David Lowry

Organization: Arizona State University

Title-Subject: [Filtered] Mycobacterium prep for immuno-label

Question: I am attempting to do thin section immuno-labeling experiments with Mycobacterium tuberculosis. I have used standard procedures: fixation with 4% paraformaldehyde/0.1% glut, then enmeshed cells in ~ 1% agarose prior to EtOH dehydration and LR White resin. Very basic stuff.

Unfortunately, in 2 separate trials I have encountered a problem with very large holes in the resin around and between the clusters of cells. It seems to be either incomplete dehydration or poor penetration of resin, although in both attempts I used 100% EtOH dehydration and extensive time in 100% LR.

Are there special considerations to take when working with this organism? I have searched on-line for information but could not locate any specific indications. I suspect there may be something unusual about the outer cell boundary that is causing this problem, and would like to know if anyone may have experience in dealing with this organism.

Thank you

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From: nizets2-at-yahoo.com
Date: Tue, 17 Apr 2007 04:46:03 -0500
Subject: [Microscopy] Hoechst Vs DAPI staining

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Thanks Vlad. I did realize that some of these alternatives would not
work for my application, but wanted to list them for others (ie, Nanovan
is an alternative to UA as a negative stain, not for sections, as you
point out). I do plan on continuing to educate people here on UA, but
sometimes these things are political, rather than scientific.

Thanks again,
Jessica Cervantes

-----Original Message-----
X-from: Vlad Speransky [mailto:vladislav_speransky-at-nih.gov]
Sent: Monday, April 16, 2007 11:59 AM
To: Cervantes, Jessica

Dear colleagues,

Usually to observe apopototic patterns in fluorescence
microscopy the most straigthforward method is to label
the cell nuclei with Hoechst. I very rarely noticed
that DAPI was used. Why?
Is there a reason why Hoechst should be preferred to
DAPI?

Stephane, epifluorescer not confocaler (or is it
confocaliser?)


__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com

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From: oshel1pe-at-cmich.edu
Date: Tue, 17 Apr 2007 07:25:57 -0500
Subject: [Microscopy] Hayat & Miller "Negative Staining"

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List,

Anyone have a copy in good or better condition of Hayat & Miller,
"Negative Staining" that they want to sell? I can only find one on
the web at an outrageous price. This is for the lab out of my pocket,
so price is also important.
Be nice if they put out a 2nd edition (hint, hint).
Thanks.

Phil
--
Philip Oshel
Microscopy Facility Supervisor
Biology Department
024C Brooks Hall
Central Michigan University
Mt. Pleasant, MI 48859
voice: (989) 774-3576
dept. fax: (989) 774-3462

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From: eschumacher-at-mccrone.com
Date: Tue, 17 Apr 2007 07:30:13 -0500
Subject: [Microscopy] Meeting: M3S Optical Techniques Workshop

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Greetings Colleagues,

The next meeting of the Midwest Microscopy and Microanalysis Society, an
Optical Techniques Workshop, will be held on Thursday, May 17, at the
College of Microscopy in Westmont, IL (The McCrone Group). Please
follow the link below and click on Meetings for program details and
registration information.

www.midwestmicroscopy.org

We look forward to seeing you there.

Elaine Schumacher
President, Midwest Microscopy and Microanalysis Society
elaine-at-midwestmicroscopy.org



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From: rpowell-at-nanoprobes.com
Date: Tue, 17 Apr 2007 08:25:44 -0500
Subject: [Microscopy] viaWWW: TEM:Alternatives to Uranyl Acetate Stain

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Email: rpowell-at-nanoprobes.com
Name: Rick Powell

Organization: Nanoprobes, Incorporated

Title-Subject: [Filtered] TEM:Alternatives to Uranyl Acetate Stain

Question: Hello Everyone:

In my somewhat hasty response to Jessica Cervantes, I had overlooked the fact that the original post referred to poststaining (positive staining) of sections. To clarify, our NanoVan and Nano-W products are intended as negative stains for protein complexes, viruses, etc.; we are not aware of any references that describe their use on thin sections.

If anyone has tried this, or has seen any references, we would of course very much like to know.

Regards,

Rick Powell

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From: gwe-at-ufl.edu
Date: Tue, 17 Apr 2007 09:19:16 -0500
Subject: [Microscopy] Video Catalog

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The MSA video catalog is currently unavailable online . It had been
hosted at the University of Florida, Biotech Center. They are totally
revamping their web site and many things have not yet been restored to
active status. I have arranged with Nestor to have the catalog hosted
on the MSA server. AS soon as I clean up the file a bit, Nestor will be
able to get it up and running and accessible from the MSA main page. In
the meantime, if you need any info about the video collection, please
feel free to email me.
The "Tips & Tricks" page that was hosted by the EM Core Lab at Florida
is also offline. I am told that it will eventually be restored.
Stay tuned.

Greg
--
Greg Erdos
University of Florida, Retired
Micanopy, Florida

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From: gmartens-at-interchange.ubc.ca
Date: Tue, 17 Apr 2007 11:22:48 -0500
Subject: [Microscopy] FISH followed by EM

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Hi everyone,

I have a request from a client who wants to localize a gene locus
within the nucleus using FISH but then wants to determine better
resolution with TEM. My first reaction would be that the FISH
protocol would destroy the ultrastructure but thought I would ask the
bigger brain if anyone out there has done something similar. I have
read a couple of papers that have done this but I was not impressed
with the ultrastructure. All thoughts are appreciated.

Garnet

--
Garnet Martens

Research Manager
BioImaging Facility
University of British Columbia
6270 University Blvd.
Vancouver, B.C.
Canada
V6T 1Z4

phone 604-822-3354

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From: bfoster-at-mme1.com
Date: Tue, 17 Apr 2007 12:11:16 -0500
Subject: [Microscopy] Re: FISH followed by EM

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi, Garnet

There is a intriguing new technique that combines AFM with
ultramicrotomy that images from the block face. Some of the early
work, done by Dr. Anton Efimov of NT-MDT (efimov-at-ntmdt.ru) shows very
delicate ultrastructure (~2-6nm structures) . The advantage is that
this system uses local differences in elasticity to image, rather
than heavy metal staining. You can do serial sections and, while the
AFM images from the block face, the slices are available for
conventional imaging with any sort of microscopy.

Might be an interesting alternative. Suggest that you write directly
to Dr. Efimov for further information.

Best regards,
Barbara Foster, President

Microscopy/Microscopy Education
313 S Jupiter Rd, Suite 100
Allen, TX 75002
P: 972-954-8011
W: www.MicroscopyEducation.com


MME is now scheduling customized, on-site courses through July. Call
us today for details.

P. S.
Need a good general reference or light microscopy text for next
semester? Call us today to learn more about "Optimizing LIght
Microscopy". Copies still available through MME... even for
class-room lots ... and we give quantity discounts. Call Ken Piel at
(972)954-8011.


At 12:05 PM 4/17/2007, gmartens-at-interchange.ubc.ca wrote:



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From: mike.reedy-at-cellbio.duke.edu
Date: Tue, 17 Apr 2007 19:40:31 -0500
Subject: [Microscopy] RE: TEM: Alternative to Uranyl Acetate Stain

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Jessica
Don't know about KMnO4 staining compatibility
with LR White; please let me know. The easy test
is to put a blank block or chunk or flake of
cured LR White in 1-2% KMnO4 and soak it for an
hour or a day to see if resin surface turns light
brown, dark brown, or black and charred looking.
No reaction is good news for section staining.

The more stringent assay for reaction is to put
the test tube of KMnO4 solution with the cured
embedding resin in a beaker of water and then
heat the water to boiling for an hour or so, cool
it off and examine the resin surface for such
changes. Araldite 506 (lowest viscosity one I
know of) and other Araldites used for embedding
are remarkable resistant to surface discoloration
when this is done. Epon DDSA (no MNA; fiddle
the mix until it is hard enough to please you,
and forget the epoxy:anhydride ratio lore) turns
moderately browner, as I recall, but is still
acceptable for section staining, with some
tendency to be more granular and maybe show some
hard-to-eliminate nano-pepper stain deposit in
contrast to Araldite.

LR White is an acrylic says EMS:
LR White is a polar monomer polyhydroxylated
acromatic acrylic resin. It can be cured by heat
or by UV light. Sections of polymerized LR White
resin are hydrophilic
I think Lawn's 1960 JCB paper introducing KMnO4
section staining used sections of methacrylate,
the mix of methyl and butyl methacrylate we all
used in the late 1950s before epoxies, especially
Epon, turned up and became dominant.

BTW-- tannic acid is a fixative and a mordant,
and magically capable of superior structure
preservation and assuring really strong uniform
staining in our hands-- see the evidence of 13Å
preservtion in fiber x-ray diffraction from
fixed-embedded fibers in Sader et al 2007 in J
Struct Biol (Articles In Press on line), and
look at EMs in some reprints I sent you for
evidence of the good morphology. The latter is
a wondrous gift of TA I had no idea of until I
learned it from David Begg et al, J. Cell Biol.
79:846-852, an all-time key paper in my book of
methodological turning points.. The other key
was the observation by Hirose and Wakabayashi (J.
Mol. Biol. 204:797-801) that TA followed by OsO4
or UrAc give great morphological fixation without
aldehydes. They used it for freeze-substitution,
as we have, but we found it also worked very well
as a general fix (we termed this TAURAC) for
permeabilized cells in aqueous buffers so long as
we exluded TA blockers like PVP, Triton X 100 etc.

Your UA police might be interested in a demo of
how completely tannins, esp tannic acid, can
convert a UrAc solution into a flocculent brown
precipitate at the bottom of a UrAc-free
supernatan (it LOOKS UrAc free! I made no
measurements.). TA is cheap in non-EM grades;
maybe they'd accept precipitation as a way of
rendering it safely bio-inactive. From the
information online at EMS ib their
datasheet/22400, I've estimated that the 10,400
counts/secin depleted uranium is reduced to about
-2 ct/sec in a very small bundle of muscle fibers
containing 1 ug of protein and binding maybe 5 ug
of UrAc. But it still requires health police and
special containment if such a specimen is to be
transported into or within the DOE facility at
Argonne National Laboratory. The inconvenience
has so far discouraged me from pursuing some
experiments that would require such a specimen,
but one day I will do it, legally and according
to their regulations. I doubt a Geiger counter
could detect any rise above background in the
presence of that small an amount of UrAc.

-mike-


} Thanks for this Mike. I think KMnO4 followed by Sato's is one of the
} better alternatives I've seen so far. Your results are very impressive.
}
}
} Any idea if KMnO4 will work with LR White embedded tissues?
}
} Thanks,
} Jessica Cervantes
} Bend Research Inc
}
} -----Original Message-----
} From: Mike Reedy [mailto:mike.reedy-at-cellbio.duke.edu]
} Sent: Saturday, April 14, 2007 5:19 PM
} To: Cervantes, Jessica
} Subject: Re: [Microscopy] TEM: Alternative to Uranyl Acetate Stain
}
} You will get even more contrast if you use KMnO4 followed by Sato's,
} as we have since 1964 (when Pb was was Pb cittrate, not Sato's).
} And, you can get good contrast on thinner sections. Using Tannic
} acid in the block stain, before OSO4, or after but followed by UrAc,
} adds to contrast, improves preservation. We have had excellent
} results (see attached).
}
} Some reports of using TA as a section stain before Pb stain can also
} be found with google help. I've never tried it yet.
}
} KMnO4 section stain won't work if NMA is in your Epon mix. see
} attached.
} -mike reedy-
} } -----------------------------------------------------------------------
} -----
} } The Microscopy ListServer -- CoSponsor: The Microscopy Society of
} America


--
-mike reedy-

************************
Michael K. Reedy, M.D.
Duke Univ. Med. Center
Dept. Cell Biology, Box 3011 (for U.S. Mail)
458 Alex Sands Bldg, Research Dr (courier)
Durham, NC 27710

Office 919-668-2534
Lab 919-684-5674
Fax 919-681-9929
mike.reedy-at-cellbio.duke.edu
http://note.cellbio.duke.edu/Faculty/Research/Reedy.html


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From: mike.reedy-at-cellbio.duke.edu
Date: Tue, 17 Apr 2007 19:43:17 -0500
Subject: [Microscopy] RE: TEM: Alternative to Uranyl Acetate Stain

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Jessica
sorry to resend all that. I am trying to see if I can calm the HTML
detector to break through into the list server,
--
-mike reedy-

************************
Michael K. Reedy, M.D.
Duke Univ. Med. Center
Dept. Cell Biology, Box 3011 (for U.S. Mail)
458 Alex Sands Bldg, Research Dr (courier)
Durham, NC 27710

Office 919-668-2534
Lab 919-684-5674
Fax 919-681-9929
mike.reedy-at-cellbio.duke.edu
http://note.cellbio.duke.edu/Faculty/Research/Reedy.html

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From: Niraj.Trivedi-at-childrens.harvard.edu
Date: Tue, 17 Apr 2007 20:15:20 -0500
Subject: [Microscopy] viaWWW: NESM 2007 Woods Hole Meeting

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Email: Niraj.Trivedi-at-childrens.harvard.edu
Name: Niraj Trivedi

Organization: New England Society of Microscopy

Title-Subject: [Filtered] NESM 2007 Woods Hole Meeting

Question: Please join us for the New England Society of Microscopy's (NESM)24th Annual Woods Hole Meeting, where we will be celebrating NESM's 40th birthday!

Expect very exciting talks and a special presentation from most of the past presidents.

Please see the link to the newsletter for more information:

http://nesm.cims.harvard.edu/Newsletters/2007_April_Newsletter.pdf

--Niraj

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From: allan.mitchell-at-stonebow.otago.ac.nz
Date: Tue, 17 Apr 2007 22:11:32 -0500
Subject: [Microscopy] RE: TEM: Alternative to Uranyl Acetate Stain

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi all

Been away so missed the original question but has any one suggested p-
Phenylenediamine?

Numerous references to using p-phenylenediamine but one to start
with is "The use of p-phenylenediamine in the block to enhance
osmium staining for electron microscopy" Stain Technology, Vol 47,
No5 pp 239 - 243.

Added in the 70% ethanol dehydration step from memory.

Regards

Allan



Allan Mitchell
technical Manager
Otago Centre for Electron Microscopy
Department of Anatomy and Structural Biology
School of Medical Sciences
P.O. Box 913
Dunedin
New Zealand

Phone (03) 479 5642 or 479 7301
Fax (03) 479 5086 or 479 7254

EM Centre: http://ocem.otago.ac.nz/
Confocal Centre: http://occm.otago.ac.nz/
Department: http://anatomy.otago.ac.nz/


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From: nizets2-at-yahoo.com
Date: Wed, 18 Apr 2007 08:04:09 -0500
Subject: [Microscopy] aluminosilicate and BSE

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Dear Listers,

I want to detect aluminosilicate particles in the
middle of organic material. The particles are expected
to be too small for light microscopy and too dilute
for TEM. The solution would be to dry everything flat
on a SEM stub and to find a way to differentiate
organic particles for aluminosilicate particles.
Our EDX doesn't want to start so I wondered if I could
see something with BSE?
X-from the atomic weight of the elements, Al and Si are
not particularly heavy but they are of course very
dense in the particles.
Do you think it would be possible? Any remark?

Stephane



__________________________________________________
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From: petra.wahlbring-at-goodyear.com
Date: Wed, 18 Apr 2007 08:23:11 -0500
Subject: [Microscopy] Re: aluminosilicate and BSE

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Dear Stephane,

if you own a decent BSE detector, I'm sure that you will be able to see a
contrast between the two types of particles. Average atomic number is well
apart from each other. To make the observation easier, I would recommend to
use a low-Z SEM stub like graphite or a graphite plate on top of a standard
holder. Then you will be able to see your silicates with a bright contrast
with respect to the background and the other particles.

Best regards,

Petra
---------------------------------------
Dr. Petra Wahlbring
Goodyear S.A. Technical Center
Analytical Test Laboratories
L-7750 Colmar-Berg
Luxembourg
Tel +352 8199 3725
Fax +352 8199 3905
e-mail: petra.wahlbring-at-goodyear.com

- May Contain Confidential and/or Proprietary Information. May not be
copied or disseminated without the expressed written consent of The
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nizets2-at-yahoo.com

04/18/07 03:09 PM To
petra.wahlbring-at-goodyear.com
cc
Please respond to
nizets2-at-yahoo.com Subject
[Microscopy] aluminosilicate and
BSE














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Dear Listers,

I want to detect aluminosilicate particles in the
middle of organic material. The particles are expected
to be too small for light microscopy and too dilute
for TEM. The solution would be to dry everything flat
on a SEM stub and to find a way to differentiate
organic particles for aluminosilicate particles.
Our EDX doesn't want to start so I wondered if I could
see something with BSE?
X-from the atomic weight of the elements, Al and Si are
not particularly heavy but they are of course very
dense in the particles.
Do you think it would be possible? Any remark?

Stephane



__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com

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From: tauria-at-hotmail.com
Date: Wed, 18 Apr 2007 08:33:16 -0500
Subject: [Microscopy] AskAMicroscopist: OPERATING MANUAL FOR A PERKIN ELMER INFRARED

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Below is the result of your feedback form (NJZFM-ultra-55). It was submitted by (tauria-at-hotmail.com) from http://www.microscopy.com/Ask-A-Microscopist/Ask-A-Microscopist.html on Wednesday, April 11, 2007 at 12:33:00
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Email: tauria-at-hotmail.com
Name: DR. FRANCIS J. PRONESTI

Organization: WORLD ENERGY SERVICES, LTD.

Education: Graduate College

Location: castellana grotte, bari, italy

Question: HELLO EVERYONE,
I NEED URGENTLY AN OPERATING MANUAL FOR A PERKIN ELMER INFRARED MICROSCOPE,MODEL FT-IR, S/N 144235 MANUFACTURED IN 1991. PART NO. N187-3065.
THANKS AND KIND REGARDS TO ALL.
DR. FRANCIS J. PRONESTI


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From: akoorts-at-medic.up.ac.za
Date: Wed, 18 Apr 2007 08:33:50 -0500
Subject: [Microscopy] AskAMicroscopist: count gold particles

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This Question was submitted to Ask-A-Microscopist by (akoorts-at-medic.up.ac.za)
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Email: akoorts-at-medic.up.ac.za
Name: Alida Koorts

Organization: University of Pretoria

Education: Graduate College

Location: Pretoria, South Africa

Question: Are there any software available to count gold particles (immunolocalization) on TEM photo's?

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From: mcauliff-at-umdnj.edu
Date: Wed, 18 Apr 2007 08:58:20 -0500
Subject: [Microscopy] Re: Alternative to Uranyl Acetate Stain/p-phenylene

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Allan Micthell suggested para-phenylene diamine as an osmium
'enhancer' and I agree. I have used p-pd in 70% ethanol during
dehydration for years, it chemically reduces osmium bound to the tissue
and increases contrast. The only drawback is that tissue so treated is
difficult to stain with the usual toluidine blue + borax solution.

Geoff


allan.mitchell-at-stonebow.otago.ac.nz wrote:

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From: mike.reedy-at-cellbio.duke.edu
Date: Wed, 18 Apr 2007 10:11:53 -0500
Subject: [Microscopy] RE: TEM: Alternative to Uranyl Acetate Stain

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Jessica
Don't know about KMnO4 staining compatibility
with LR White; please let me know. The easy test
is to put a blank block or chunk or flake of
cured LR White in 1-2% KMnO4 and soak it for an
hour or a day to see if resin surface turns light
brown, dark brown, or black and charred looking.
No reaction is good news for section staining.

The more stringent assay for reaction is to put
the test tube of KMnO4 solution with the cured
embedding resin in a beaker of water and then
heat the water to boiling for an hour or so, cool
it off and examine the resin surface for such
changes. Araldite 506 (lowest viscosity one I
know of) and other Araldites used for embedding
are remarkable resistant to surface discoloration
when this is done. Epon DDSA (no MNA; fiddle
the mix until it is hard enough to please you,
and forget the epoxy:anhydride ratio lore) turns
moderately browner, as I recall, but is still
acceptable for section staining, with some
tendency to be more granular and maybe show some
hard-to-eliminate nano-pepper stain deposit in
contrast to Araldite.

LR White is an acrylic says EMS:
LR White is a polar monomer polyhydroxylated
acromatic acrylic resin. It can be cured by heat
or by UV light. Sections of polymerized LR White
resin are hydrophilic
I think Lawn's 1960 JCB paper introducing KMnO4
section staining used sections of methacrylate,
the mix of methyl and butyl methacrylate we all
used in the late 1950s before epoxies, especially
Epon, turned up and became dominant.

BTW-- tannic acid is a fixative and a mordant,
and magically capable of superior structure
preservation and assuring really strong uniform
staining in our hands-- see the evidence of 13Å
preservtion in fiber x-ray diffraction from
fixed-embedded fibers in Sader et al 2007 in J
Struct Biol (Articles In Press on line), and
look at EMs in some reprints I sent you for
evidence of the good morphology. The latter is
a wondrous gift of TA I had no idea of until I
learned it from David Begg et al, J. Cell Biol.
79:846-852, an all-time key paper in my book of
methodological turning points.. The other key
was the observation by Hirose and Wakabayashi (J.
Mol. Biol. 204:797-801) that TA followed by OsO4
or UrAc give great morphological fixation without
aldehydes. They used it for freeze-substitution,
as we have, but we found it also worked very well
as a general fix (we termed this TAURAC) for
permeabilized cells in aqueous buffers so long as
we exluded TA blockers like PVP, Triton X 100 etc.

Your UA police might be interested in a demo of
how completely tannins, esp tannic acid, can
convert a UrAc solution into a flocculent brown
precipitate at the bottom of a UrAc-free
supernatan (it LOOKS UrAc free! I made no
measurements.). TA is cheap in non-EM grades;
maybe they'd accept precipitation as a way of
rendering it safely bio-inactive. From the
information online at EMS ib their
datasheet/22400, I've estimated that the 10,400
counts/secin depleted uranium is reduced to about
-2 ct/sec in a very small bundle of muscle fibers
containing 1 ug of protein and binding maybe 5 ug
of UrAc. But it still requires health police and
special containment if such a specimen is to be
transported into or within the DOE facility at
Argonne National Laboratory. The inconvenience
has so far discouraged me from pursuing some
experiments that would require such a specimen,
but one day I will do it, legally and according
to their regulations. I doubt a Geiger counter
could detect any rise above background in the
presence of that small an amount of UrAc.

-mike-


} Thanks for this Mike. I think KMnO4 followed by Sato's is one of the
} better alternatives I've seen so far. Your results are very impressive.
}
}
} Any idea if KMnO4 will work with LR White embedded tissues?
}
} Thanks,
} Jessica Cervantes
} Bend Research Inc
}
} -----Original Message-----
} From: Mike Reedy [mailto:mike.reedy-at-cellbio.duke.edu]
} Sent: Saturday, April 14, 2007 5:19 PM
} To: Cervantes, Jessica
} Subject: Re: [Microscopy] TEM: Alternative to Uranyl Acetate Stain
}
} You will get even more contrast if you use KMnO4 followed by Sato's,
} as we have since 1964 (when Pb was was Pb cittrate, not Sato's).
} And, you can get good contrast on thinner sections. Using Tannic
} acid in the block stain, before OSO4, or after but followed by UrAc,
} adds to contrast, improves preservation. We have had excellent
} results (see attached).
}
} Some reports of using TA as a section stain before Pb stain can also
} be found with google help. I've never tried it yet.
}
} KMnO4 section stain won't work if NMA is in your Epon mix. see
} attached.
} -mike reedy-
} } -----------------------------------------------------------------------
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--
-mike reedy-

************************
Michael K. Reedy, M.D.
Duke Univ. Med. Center
Dept. Cell Biology, Box 3011 (for U.S. Mail)
458 Alex Sands Bldg, Research Dr (courier)
Durham, NC 27710

Office 919-668-2534
Lab 919-684-5674
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From: drk-at-SHCC.org
Date: Wed, 18 Apr 2007 12:43:19 -0500
Subject: [Microscopy] stabilization ofmembranes

Contents Retrieved from Microscopy Listserver Archives
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That would be a good place to start. I have posted some quite images of
inclusions in an organic goo on our web site
(ftp://www.marl.iastate.edu/Interesting/Residue/) . The mineral
inclusions show up nicely.

Another poster mentioned doing this on a carbon substrate. In fact, I
prepared this sample twice - once on a carbon stub and once on an
aluminum stub. I wanted to see how much signal was coming from below.
That was mostly for EDS and did appreciably affect the images. If you
had a mixture of particles only, the situation might be a little
different and I would recommend the dark background of a carbon
substrate.

You may run up against resolution limits for BSE depending on particle
size. The images may not be particularly sharp due to the sizeable
interaction volume and the high currents typically required for BSE.
These images were collected at 25mm WD with a sizeable current for
simultaneous EDS. You could improve resolution by cutting the working
distance and reducing current as much as possible while still
maintaining signal strength.

Warren Straszheim
Materials Analysis and Research Lab
Iowa State University

-----Original Message-----
X-from: nizets2-at-yahoo.com [mailto:nizets2-at-yahoo.com]
Sent: Wednesday, April 18, 2007 8:05 AM
To: wesaia-at-iastate.edu

Fellow Microscopists,


A few days ago I posted a query for suggestions on how to stabilize
lysosomal membranes in cultured cells prior to immunocytochemistry. We have
tried several of the tips but without success. Thanks to those who replied!
We have been following the condition of the lysosomes using a GFP tag that
we know to be specifically compartmentalized. We note that following
fixation and a rinse in TRIS-Glycine the GFP is still compartmentalized.
However, perhaps in 90% EtOH and definitely in 1:1 LR White:90% EtOH we see
the GFP moves from the lysosomes to the cytoplasm and nucleus. It seems that
ethanol and certainly LR White contribute to the deterioration of membranes.
Can anyone suggest an embedding media that might be a little gentler on
membranes and still possibly work for surface label immunocytochemistry? We
are thinking of trying Nanoplast, a water soluble media but any suggestions
are welcome.


Thanks! Doug

Douglas R. Keene
Assistant Investigator
Micro-Imaging Center
Shriners Hospital for Children
3102 S.W. Sam Jackson Park Road
Portland, Oregon 97239
503-221-3434
drk-at-shcc.org


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From: mnesta-at-ebsciences.com
Date: Wed, 18 Apr 2007 13:59:20 -0500
Subject: [Microscopy] SEM Accessory Sales Position Opening

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Energy Beam Sciences, Inc. is seeking a Technical Sales Representative
with a background in Scanning Electron Microscopy to represent an
exciting line of imaging, measurement and analysis software that is new
to our Company. This is a full time position that will entail
significant travel and frequent Customer interaction. For detailed
information about this great opportunity please visit us on the web at
http://www.ebsciences.com/jobs.html.

Sincerely,

Michael R. Nesta
Managing Director
Energy Beam Sciences, Inc.
Tel: 860 653-0411
Fax: 860 653-0422
MNesta-at-ebsciences.com
www.ebsciences.com
“ADDING BRILLIANCE TO YOUR VISION”



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From: David.Patton-at-uwe.ac.uk
Date: Thu, 19 Apr 2007 05:29:37 -0500
Subject: [Microscopy] TEM: Alternative to Uranyl Acetate Stain

Contents Retrieved from Microscopy Listserver Archives
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We get nice contrast with 1% potassium permanganate (aq) followed by
lead citrate. It is good for membranes. In the past we have made it up
in 0.1M phosphate buffer at pH below 6.5 to avoid precipitates.

Dave

-----Original Message-----
X-from: cervantes-at-bendres.com [mailto:cervantes-at-bendres.com]
Sent: 13 April 2007 21:16
To: David Patton

Due to some bureaucratic mumbo-jumbo, I am not able to use Uranyl
Acetate (nuclear warheads, blah, blah, blah). I would like to stain
some osmium-fixed tissue thin-sections for TEM; the procedure I'm
following has a UA/Sato's lead stain step for the sections. Does anyone
know of a suitable alternative? I did a quick google and listserver
archive search and didn't find anything, but I'm hoping someone has run
into this problem before and can suggest something.

Crossing my fingers,
Jessica Cervantes
Bend Research, Inc
Bend, OR


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From: David.Patton-at-uwe.ac.uk
Date: Thu, 19 Apr 2007 09:51:25 -0500
Subject: [Microscopy] RE: TEM: Alternative to Uranyl Acetate Stain

Contents Retrieved from Microscopy Listserver Archives
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Sorry - just back from leave! Recently we have used it on 20yr old
epoxy blocks of unknown provenance and TAAB embedding resin. No
experience on LR White.

Will try Pal's bleach as we seem to have some non-specific staining.

It was in use here in 1989, when I started here, due to a safety scare
(yes even back in the good old days!). Hayat (1989) noted precipitates
above pH 6.8. We have never investigated the maintainance of pH. We
stain for 5-10min with KMnO4.

Dave



-----Original Message-----
X-from: Mike Reedy [mailto:mike.reedy-at-cellbio.duke.edu]
Sent: 19 April 2007 15:20
To: David Patton
Cc: cervantes-at-bendres.com


--
-mike reedy-

************************
Michael K. Reedy, M.D.
Duke Univ. Med. Center
Dept. Cell Biology, Box 3011 (for U.S. Mail)
458 Alex Sands Bldg, Research Dr (courier)
Durham, NC 27710

Office 919-668-2534
Lab 919-684-5674
Fax 919-681-9929
mike.reedy-at-cellbio.duke.edu
http://note.cellbio.duke.edu/Faculty/Research/Reedy.html

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From: paul_hazelton-at-umanitoba.ca
Date: Thu, 19 Apr 2007 12:40:16 -0500
Subject: [Microscopy] nova operator's manual

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Wim -

Here's the list of references. I haven't checked if all are available
or still in print.

I'm replying to the whole list in case anyone else is interested (can't
tell if you sent your message just to me).

Jessica Cervantes
Bend Research Inc
Bend, OR


The Cell, by Don W. Fawcett, MD. W. B. Saunders Company (out of
print).

Biomedical Electron Microscopy - Illustrated Methods and
Interpretations, by Arvid B. Maunsbach and Bjorn A. Afzelius. Academic
Press; 1st edition (January 15, 1999).

Cell and tissue ultrastructure: a functional perspective, by P. C.
Cross, and K. L. Mercer. W. H. Freeman & Co, 1993. 420 pp.

Histology: A text and Atlas, by Michael H. Ross, and Wojciech Pawlina.
Lippincott Williams & Wilkins; 1st edition (December 1, 2005). Was
updated 2006 (paperback) with CD-ROM and is available from Barnes &
Noble.

Color Atlas of Cytology, Histology and Microscopic Anatomy, by Wolfgang
Kuehnel. Thieme Medical Publishers; 4th edition (July 2003).

An Atlas of Ultrastructure, by Johannes Rhodin. W.B. Saunders Co.

Bloom and Fawcett: Concise Histology, by Don W. Fawcett, Ronald P.
Jensh. A Hodder Arnold Publication; 2nd edition (June 15, 2002).

For plant cells:
Introduction to the Fine Structure of Plant Cells, Myron Ledbetter and
Keith Porter. Springer-Verlag.



-----Original Message-----
X-from: Prof. dr. Wim Van den Broeck [mailto:wim.vandenbroeck-at-UGent.be]
Sent: Thursday, April 19, 2007 12:29 AM
To: Cervantes, Jessica

It seems that I've just been gifted with an LKB Nova ultratome, complete
with hydrolic table. However, there are no operator's manuals with the
microtome. Set it up and it is working fine, but would really like to
have an operator's manual so that I can check and make sure we know all
the little ins and outs of the machine.

Can any one help?????

Paul



Paul R. Hazelton, PhD
Electron Microscope Unit
University of Manitoba
Department of Medical Microbiology
531 Basic Medical Sciences Building
730 William Avenue
Winnipeg, Manitoba, Canada, R3E 0W3
e-mail: paul_hazelton-at-umanitoba.ca
Phone:204-789-3313
Pager:204-931-9354
Cell:204-781-1502
Fax:204-789-3926









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From: scott.streiker-at-udri.udayton.edu
Date: Thu, 19 Apr 2007 14:41:43 -0500
Subject: [Microscopy] viaWWW: Uptake of nanoparticles in cells using TEM

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Email: scott.streiker-at-udri.udayton.edu
Name: Scott Streiker

Organization: University of Dayton Research Institute

Title-Subject: [Filtered] Uptake of nanoparticles in cells using TEM

Question: Hello! I am trying to visualize the uptake of nanomaterials in cells using TEM. I have a cell pellet that I would like to embed in resin and then section using the ultramicrotome. One kit that I have the option to use is the Epofix Cold-Setting Resin from EMS. Has anyone used this kit before on biological samples? Or is there a better resin to try?

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From: bfoster-at-mme1.com
Date: Thu, 19 Apr 2007 16:44:57 -0500
Subject: [Microscopy] Re: viaWWW: Uptake of nanoparticles in cells

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html


For plant cells there are also books by Brian Gunning

Brian E.S Gunning and Martin W. Steer 'Plant Cell Biology; Structure and
Function' Jones and Bartlett Publishers (1996)

Brian E.S Gunning and Martin W. Steer 'Ultrastructure and the Biology of
Plant Cells' Edward Arnold (older version from mid 1970's

There is also a new DVD due out mid 2007 (I have seen an early version
which looks very good). You can find information
at:www.plantcellbiologyondvd.com/default.cfm

Ian

Ian Hallett
Sensory and Consumer Science - Microscopy
HortResearch, Mt Albert Research Centre
Private Bag 92 169, Auckland Mail Centre
Auckland 1142, New Zealand
+64-9-815 4200 ext 7002

-----Original Message-----
X-from: cervantes-at-bendres.com [mailto:cervantes-at-bendres.com]
Sent: Friday, 20 April 2007 3:35 a.m.
To: Ian Hallett

Wim -

Here's the list of references. I haven't checked if all are available
or still in print.

I'm replying to the whole list in case anyone else is interested (can't
tell if you sent your message just to me).

Jessica Cervantes
Bend Research Inc
Bend, OR


The Cell, by Don W. Fawcett, MD. W. B. Saunders Company (out of
print).

Biomedical Electron Microscopy - Illustrated Methods and
Interpretations, by Arvid B. Maunsbach and Bjorn A. Afzelius. Academic
Press; 1st edition (January 15, 1999).

Cell and tissue ultrastructure: a functional perspective, by P. C.
Cross, and K. L. Mercer. W. H. Freeman & Co, 1993. 420 pp.

Histology: A text and Atlas, by Michael H. Ross, and Wojciech Pawlina.
Lippincott Williams & Wilkins; 1st edition (December 1, 2005). Was
updated 2006 (paperback) with CD-ROM and is available from Barnes &
Noble.

Color Atlas of Cytology, Histology and Microscopic Anatomy, by Wolfgang
Kuehnel. Thieme Medical Publishers; 4th edition (July 2003).

An Atlas of Ultrastructure, by Johannes Rhodin. W.B. Saunders Co.

Bloom and Fawcett: Concise Histology, by Don W. Fawcett, Ronald P.
Jensh. A Hodder Arnold Publication; 2nd edition (June 15, 2002).

For plant cells:
Introduction to the Fine Structure of Plant Cells, Myron Ledbetter and
Keith Porter. Springer-Verlag.



-----Original Message-----
X-from: Prof. dr. Wim Van den Broeck [mailto:wim.vandenbroeck-at-UGent.be]
Sent: Thursday, April 19, 2007 12:29 AM
To: Cervantes, Jessica

Hi, Scott

This would definitely be another of those interesting applications to
try with the new Tomo AFM/Ultramicrotome from NT-MDT. The AFM is
superb at imaging nanoparticles and TOMO uses the Leica
ultramicrotome for sectioning.

While I don't have any pictures of nanoparticles, I do have a really
neat movie I can share with you showing the serial sectioning of
nanotubes in epoxy, followed by the dynamic 3D reconstruction from
Dr. DeWith at the Dutch Polymer Institute at the
TU/Eindhoven. Contact me off-line if you are interested. I can
send it via YouSendIt so that you can download it easily. Also, if
you are interested in seeing if this is a good solution for your
application, I encourage you to correspond directly with Dr. Efimov
at NTMDT (see CC above). He may be able to run a sample for you.

Hope this is helpful.

Best regards,
Barbara Foster

Microscopy/Microscopy Education
313 S Jupiter Rd, Suite 100
Allen, TX 75002
P: 972-954-8011
W: www.MicroscopyEducation.com

Caveat: MME is working with NTMDT in support of the TOMO.

MME is now scheduling customized, on-site courses through July. Call
us today for details.

P. S.
Need a good general reference or light microscopy text for next
semester? Call us today to learn more about "Optimizing LIght
Microscopy". Copies still available through MME... even for
class-room lots ... and we give quantity discounts. Call Ken Piel at
(972)954-8011.

At 04:16 PM 4/19/2007, scott.streiker-at-udri.udayton.edu wrote:



} ----------------------------------------------------------------------------
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From: eknoppel-at-cc.usu.edu
Date: Thu, 19 Apr 2007 16:57:51 -0500
Subject: [Microscopy] viaWWW: Lung tissue

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Email: eknoppel-at-cc.usu.edu
Name: Edward L. Knoppel

Organization: USDA-ARS-PPRL

Title-Subject: [Filtered] Lung tissue

Question: Without using a microwave, freezing or perfusion of the tissue; is there a "really" good procedure for fixing pieces of animal lung tissue that someone would be gracious enough to share? Thanks in advance, Ed

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From: ewing.hr-at-bruker-axs.com
Date: Thu, 19 Apr 2007 16:58:33 -0500
Subject: [Microscopy] viaWWW: Job Opening: Senior Salesperson - Microanalysis

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Email: ewing.hr-at-bruker-axs.com
Name: Doug Skinner

Organization: Bruker AXS Microanalysis

Title-Subject: [Filtered] Job Opening: Senior Salesperson - Microanalysis

Question: Senior Salesperson - Microanalysis

Bruker AXS, Inc., a leading manufacturer of Analytical Instrumentation, has a job opening for a Senior Salesperson, working out of the Bruker Canada office in Milton, Ontario.

The position is to secure sales for BAXS Microanalysis Products in Canada and act as the technical sales representative to the existing customer base and prospective customers. Significant travel throughout Canada will be required.

Job responsibilities:

ï Prospecting for new customers
ï Following up sales leads provided by the company
ï Presenting and demonstrating company products
ï Supplying quotations and technical information, formulating sales strategies, as well as negotiating and securing sales orders
ï Maintain contact with existing customers to assure their satisfaction, develop good working relationships with SEM salespeople, collect and report market information and provide routine sales forecasts.

Bachelor's degree (B.S. or B.A.) from four-year College; or five years experience and/or training; or equivalent combination of education and experience. Three years experience in scientific equipment sales is desired. This position requires excellent verbal communication and interaction skills. Fluency in French and English is preferred.

Candidates meeting these requirements should send a resume to:

Doug Skinner
Bruker AXS Microanalysis
ewing.hr-at-bruker-axs.com



---------------------------------------------------------------------------


==============================Original Headers==============================
16, 13 -- From zaluzec-at-microscopy.com Thu Apr 19 16:58:32 2007
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16, 13 -- Subject: viaWWW: Job Opening: Senior Salesperson - Microanalysis
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From: cervantes-at-bendres.com
Date: Thu, 19 Apr 2007 17:57:57 -0500
Subject: [Microscopy] stabilization ofmembranes

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Did I miss the replies to this query somehow? Is there a technical
problem, or were the replies private? Would it be possible to post
them?

Let's not be shy (if that's it) about posting to the whole list. I've
gotten so much out of this resource (especially lately). I've had to
re-post replies to my query for others who have had the same question
and hadn't gotten the messages.

Thanks for keeping the information flowing; it's invaluable.
Jessica Cervantes
Bend Research Inc
Bend, OR

-----Original Message-----
X-from: drk-at-SHCC.org [mailto:drk-at-SHCC.org]
Sent: Wednesday, April 18, 2007 10:49 AM
To: Cervantes, Jessica

Fellow Microscopists,


A few days ago I posted a query for suggestions on how to stabilize
lysosomal membranes in cultured cells prior to immunocytochemistry. We
have
tried several of the tips but without success. Thanks to those who
replied!
We have been following the condition of the lysosomes using a GFP tag
that
we know to be specifically compartmentalized. We note that following
fixation and a rinse in TRIS-Glycine the GFP is still compartmentalized.
However, perhaps in 90% EtOH and definitely in 1:1 LR White:90% EtOH we
see
the GFP moves from the lysosomes to the cytoplasm and nucleus. It seems
that
ethanol and certainly LR White contribute to the deterioration of
membranes.
Can anyone suggest an embedding media that might be a little gentler on
membranes and still possibly work for surface label immunocytochemistry?
We
are thinking of trying Nanoplast, a water soluble media but any
suggestions
are welcome.


Thanks! Doug

Douglas R. Keene
Assistant Investigator
Micro-Imaging Center
Shriners Hospital for Children
3102 S.W. Sam Jackson Park Road
Portland, Oregon 97239
503-221-3434
drk-at-shcc.org


==============================Original
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7, 22 -- Date: Wed, 18 Apr 2007 10:43:58 -0700
7, 22 -- From: Doug Keene {drk-at-SHCC.org}
7, 22 -- Subject: stabilization ofmembranes
7, 22 -- Sender: drk-at-SHCC.org
7, 22 -- To: Microscopy-at-Microscopy.Com
7, 22 -- Cc: drk-at-SHCC.org
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13, 16 -- MIME-Version: 1.0
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13, 16 -- Subject: RE: [Microscopy] stabilization of membranes
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From: tom-at-tomkaye.com
Date: Thu, 19 Apr 2007 18:47:51 -0500
Subject: [Microscopy] stabilization ofmembranes

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html


I would like to 2nd the idea that replying to the list is a good thing. This
is my only resource for such information so I would rather delete than miss
an opportunity to learn something.

Thanks!

Tom Kaye

Not affiliated with anything.

-----Original Message-----
X-from: cervantes-at-bendres.com [mailto:cervantes-at-bendres.com]
Sent: Thursday, April 19, 2007 6:02 PM
To: tom-at-tomkaye.com

Did I miss the replies to this query somehow? Is there a technical
problem, or were the replies private? Would it be possible to post
them?

Let's not be shy (if that's it) about posting to the whole list. I've
gotten so much out of this resource (especially lately). I've had to
re-post replies to my query for others who have had the same question
and hadn't gotten the messages.

Thanks for keeping the information flowing; it's invaluable.
Jessica Cervantes
Bend Research Inc
Bend, OR

-----Original Message-----
X-from: drk-at-SHCC.org [mailto:drk-at-SHCC.org]
Sent: Wednesday, April 18, 2007 10:49 AM
To: Cervantes, Jessica

Fellow Microscopists,


A few days ago I posted a query for suggestions on how to stabilize
lysosomal membranes in cultured cells prior to immunocytochemistry. We
have
tried several of the tips but without success. Thanks to those who
replied!
We have been following the condition of the lysosomes using a GFP tag
that
we know to be specifically compartmentalized. We note that following
fixation and a rinse in TRIS-Glycine the GFP is still compartmentalized.
However, perhaps in 90% EtOH and definitely in 1:1 LR White:90% EtOH we
see
the GFP moves from the lysosomes to the cytoplasm and nucleus. It seems
that
ethanol and certainly LR White contribute to the deterioration of
membranes.
Can anyone suggest an embedding media that might be a little gentler on
membranes and still possibly work for surface label immunocytochemistry?
We
are thinking of trying Nanoplast, a water soluble media but any
suggestions
are welcome.


Thanks! Doug

Douglas R. Keene
Assistant Investigator
Micro-Imaging Center
Shriners Hospital for Children
3102 S.W. Sam Jackson Park Road
Portland, Oregon 97239
503-221-3434
drk-at-shcc.org


==============================Original
Headers==============================
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7, 22 -- Date: Wed, 18 Apr 2007 10:43:58 -0700
7, 22 -- From: Doug Keene {drk-at-SHCC.org}
7, 22 -- Subject: stabilization ofmembranes
7, 22 -- Sender: drk-at-SHCC.org
7, 22 -- To: Microscopy-at-Microscopy.Com
7, 22 -- Cc: drk-at-SHCC.org
7, 22 -- Reply-to: drk-at-SHCC.org
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25, 20 -- From tom-at-tomkaye.com Thu Apr 19 18:47:51 2007
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25, 20 -- From: "Tom Kaye" {tom-at-tomkaye.com}
25, 20 -- To: {microscopy-at-microscopy.com}
25, 20 -- Subject: 2nd for posting to the list
25, 20 -- Date: Thu, 19 Apr 2007 18:48:03 -0500
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From: tom-at-tomkaye.com
Date: Thu, 19 Apr 2007 19:07:06 -0500
Subject: [Microscopy] Need help with ID

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hello All,

Do any of you know what this thing is? It looks like a "bug" but it's
attached to a probable piece of fungus. Any ideas welcome, this is a head
scratcher for everyone that has seen it.

Thanks!

Tom Kaye

Tomkaye.com/images/fungus_lrg.jpg Long shot, the bug thing is lower right


Tomkaye.com/images/fungus2_lrg.jpg Close up.


==============================Original Headers==============================
8, 20 -- From tom-at-tomkaye.com Thu Apr 19 19:07:05 2007
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8, 20 -- From: "Tom Kaye" {tom-at-tomkaye.com}
8, 20 -- To: {microscopy-at-microscopy.com}
8, 20 -- Subject: Need help with ID
8, 20 -- Date: Thu, 19 Apr 2007 19:07:18 -0500
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From: Rosey.VanDriel-at-csiro.au
Date: Thu, 19 Apr 2007 23:19:42 -0500
Subject: [Microscopy] viaWWW: Lung tissue

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html


Hello Ed,
There is a method which works really well in fetal mouse lung. (Cole TJ,
Solomon NM, van Driel R, Monk JA, Bird D, Richardson SJ, Dilley RJ,
Hooper SB. Am J Respir Cell Mol Biol 2004 May; 30(5):613-9 "Altered
epithelial proportions in the fetal lung of glucocorticoid receptor null
mice")

We used the method as published by Williams, M. C. 1977. "Conversion of
lamellar body membranes into tubular myelin in alveoli of fetal rat
lungs". J. Cell Biol. 72:260-277.

It involves use of veronal (barbitone) and maleate buffers, but is
really simple to do.

However, I do not know how well it works with inflated lungs.

Briefly:
Dissect lungs from embryo, place in drop of fixative and slice gently
into mm cubes. Fix in 4% Paraformaldehyde + 2% Glutaraldehyde + 4%
Sucrose in HEPES buffered saline pH 7.4 for 3 to 4 hours at room temp.
Rinse 2 min in cold veronal acetate pH 7.4
Postfix in 1.5% OsO4 in Veronal Acetate -at- 4degrees C overnight
Rinse 3 x 10 min -at-4 deg C in Tris Maleate pH 5.2
En bloc stain with 1.5% UrAc in Tris Maleate pH5.2, 90 min on ice, in
dark
Cold dehydration, 5 minute changes in graded acetones on ice (10, 20,
30, 40, 50, 60, 70, 80, 90, 95%)Then Absolute dry acetone 4 x 10
minutes, the last 2 changes at room temp.
Absolute acetone:Epon Mix, 50:50, 30 minutes, rotating
Epon, 3 x 60 minute changes, can leave one change overnight, rotating
Embed in fresh Epon, polymerize overnight at 60 to 65 degrees C.

If you would like the buffer recipes, let me know.

Good luck!

Rosey

Rosemary van Driel
Electron Microscopy
New and Emerging Zoonotic Diseases
Australian Animal Health Laboratory
CSIRO Livestock Industries
Private Bag 24
Geelong Vic 3220
Australia

International Phone: +61 3 5227 5209
International Fax: +61 3 5227 5555
email: Rosey.VanDriel-at-csiro.au






-----Original Message-----
X-from: eknoppel-at-cc.usu.edu [mailto:eknoppel-at-cc.usu.edu]
Sent: Friday, 20 April 2007 08:00
To: Van Driel, Rosey (LI, Geelong)

This Question/Comment was submitted to the Microscopy Listserver
using the WWW based Form at
http://microscopy.com/MicroscopyListserver/MLFormMail.html
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Email: eknoppel-at-cc.usu.edu
Name: Edward L. Knoppel

Organization: USDA-ARS-PPRL

Title-Subject: [Filtered] Lung tissue

Question: Without using a microwave, freezing or perfusion of the
tissue; is there a "really" good procedure for fixing pieces of animal
lung tissue that someone would be gracious enough to share? Thanks in
advance, Ed

------------------------------------------------------------------------
---

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From: David.Patton-at-uwe.ac.uk
Date: Fri, 20 Apr 2007 03:49:14 -0500
Subject: [Microscopy] Need help with ID

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Just a guess - looks like the moulted exoskeleton of a caterpillar-like
insect larva. The nice wavy tubes look like the air circulation tubes
that connect to spiracles.

Dave

-----Original Message-----
X-from: tom-at-tomkaye.com [mailto:tom-at-tomkaye.com]
Sent: 20 April 2007 01:11
To: David Patton

Hello All,

Do any of you know what this thing is? It looks like a "bug" but it's
attached to a probable piece of fungus. Any ideas welcome, this is a
head
scratcher for everyone that has seen it.

Thanks!

Tom Kaye

Tomkaye.com/images/fungus_lrg.jpg Long shot, the bug thing is lower
right


Tomkaye.com/images/fungus2_lrg.jpg Close up.


==============================Original
Headers==============================
8, 20 -- From tom-at-tomkaye.com Thu Apr 19 19:07:05 2007
8, 20 -- Received: from tomkaye.com (mxgateway.techpro.com [64.4.207.8])
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19:07:05 -0500
8, 20 -- Received: from tk7c797a275194 [24.15.58.103] by tomkaye.com
with ESMTP
8, 20 -- (SMTPD32-8.14) id A4303503012A; Thu, 19 Apr 2007 19:07:12
-0500
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From: niko.hellsten-at-stratum.fi
Date: Fri, 20 Apr 2007 04:50:21 -0500
Subject: [Microscopy] cross section sample preparation

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hello everyone

I'm doing basic cross section preparation for light microscopy work. My
samples are stainless steel plated with 0-50 micrometers thick layers of
copper and chromium.

I would like to make the interfaces clearer than they are after
grinding/polishing. I have thought about etching/corroding the surface with
some acid or other chemical.

I would like to hear from the experts what kind of chemicals they might
recommend. Or if etching my samples chemically would do me any good at all.

Thanks in advance

Niko Hellstén
Product Engineer
Stratum Oy
mail: niko.hellsten-at-stratum.fi
GSM: +358-(0)440-955301


==============================Original Headers==============================
7, 22 -- From niko.hellsten-at-stratum.fi Fri Apr 20 04:50:21 2007
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7, 22 -- From: "Niko Hellsten" {niko.hellsten-at-stratum.fi}
7, 22 -- To: "Microscopy" {Microscopy-at-Microscopy.com}
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From: Joseph_Oparowski-at-bose.com
Date: Fri, 20 Apr 2007 06:31:22 -0500
Subject: [Microscopy] cross section sample preparation

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi

I do not know if it would be appropriate with your material but I always
suggest people fracture samples for cross section. The usual method is to
use liquid nitrogen to embrittle the specimen.

This method is mainly used for the SEM but many clients use LM as well. The
SEM is very good at detecting poor cross sections through cutting or
polishing but the fracture route has never let me down.

Steve Chapman
Senior Consultant Protrain
For electron microscopy consultancy and training world wide
Tel +44 1280 816512 Fax +44 1280 814007
Mobile +44 7711 606967 Web www.emcourses.com


----- Original Message -----
X-from: {niko.hellsten-at-stratum.fi}
To: {protrain-at-emcourses.com}
Sent: Friday, April 20, 2007 10:51 AM

Hello Niko,

If you are just trying to delineate the interfaces, I would etch the copper layer. This is assuming that your configuration is the SS base metal / a Cu under layer / a Cr outer layer. Of more importance is the polishing of the sample before etching. You must ensure that the polishing method does not introduce smearing of the polished surface, especially at the copper plating.

A flat etch to remove copper and reveal the copper grain boundaries consists of;

20 ml ammonium hydroxide
20 ml of water
5 ml of 3% hydrogen peroxide

The hydrogen peroxide is added just prior to etching. Etching is performed by swabbing the polished surface for approximately 10-30 sec.

For more on polishing methods see;

"ASM Handbook, Vol. 9 - Metallography and Microstructures", ASM International, 2004, Materials Park, OH 44073

For etchants and precautions for safely using them see;

"Metallographic Etching, 2nd Ed.", Petzow, G., ASM International, 1999, Materials Park, OH 44073


Good luck.

Joseph

Joseph M. Oparowski
Center for Materials Science
Bose Corporation Joseph_Oparowski-at-bose.com
The Mountain, M/S 415 Phone: (508) 766-1371
Framingham, MA 01701-9168 Fax: (508) 766-1313


-----Original Message-----
X-from: niko.hellsten-at-stratum.fi [mailto:niko.hellsten-at-stratum.fi]
Sent: Friday, April 20, 2007 5:55 AM
To: Oparowski, Joseph

Hello everyone

I'm doing basic cross section preparation for light microscopy work. My
samples are stainless steel plated with 0-50 micrometers thick layers of
copper and chromium.

I would like to make the interfaces clearer than they are after
grinding/polishing. I have thought about etching/corroding the surface with
some acid or other chemical.

I would like to hear from the experts what kind of chemicals they might
recommend. Or if etching my samples chemically would do me any good at all.

Thanks in advance

Niko Hellstén
Product Engineer
Stratum Oy
mail: niko.hellsten-at-stratum.fi
GSM: +358-(0)440-955301


==============================Original Headers==============================
7, 22 -- From niko.hellsten-at-stratum.fi Fri Apr 20 04:50:21 2007 7, 22 -- Received: from emh03.mail.saunalahti.fi (emh03.mail.saunalahti.fi [62.142.5.109])
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7, 22 -- From: "Niko Hellsten" {niko.hellsten-at-stratum.fi}
7, 22 -- To: "Microscopy" {Microscopy-at-Microscopy.com}
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28, 24 -- From Joseph_Oparowski-at-bose.com Fri Apr 20 06:31:21 2007
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From: klemari_cz-at-yahoo.com
Date: Fri, 20 Apr 2007 07:03:59 -0500
Subject: [Microscopy] ultramicrotome

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hello everyone,

our institution has acquired money to buy an
ultramicrotome for TEM sample preparation of material
samples, such as layered structures (clay minerals or
thin layers on Si support).

To my knowledge, there are currently two
ultramicrotomes on the market - EM UC6 from Leica and
Power-Tome XL from RMC. I have talked to sales people
from both companies, and of course they both claim
that their cutting technique is the best for cutting
hard materials because it does not introduce internal
vibrations. RMC is motor driven while Leica boasts
with "the Gravity Stroke". I can imagine both
techniques having some troubles vibrationwise so I am
torn and confused. So here comes the question. Has
anybody ever tried to section hard materials on these
machines and compared the results?

Thanks a lot for your time.

Have a nice weekend,

Mariana

¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤

Mariana Klementova
Institute of Inorganic Chemistry of the ASCR, v.v.i.
250 68 Husinec-Rez 1001
Czech Republic

phone: ++420-266 17 31 44
mobile: ++420-723 52 66 19
fax: ++420-220 94 15 02
e-mail: klemari-at-iic.cas.cz
http://www.iic.cas.cz/~jem3010/english/

¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤

__________________________________________________
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From: Walter.Bobrowski-at-pfizer.com
Date: Fri, 20 Apr 2007 07:16:29 -0500
Subject: [Microscopy] stabilization ofmembranes

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Jessica, have you attempted ICC following routine aldehyde fixation and
osmium post-fixation followed by standard epoxy embedding? The osmium
will preserve the membranes and you *may* still get successful ICC. Give
a holler and I'll send you a (work in progress) protocol that appears to
yield successful IHC on LM thick sections using RT reagents (no
microwaves, no heated steam baths).

Best regards,

Walter F. Bobrowski
Sr. Scientist
Pfizer Global R&D
2800 Plymouth Rd.
Ann Arbor, MI 48105

TEL: 734-622-7814
FAX: 734-622-5718

"The ultimate human freedom is the ability to choose one's attitude in a
given set of circumstances." -Viktor Frankl



-----Original Message-----
X-from: cervantes-at-bendres.com [mailto:cervantes-at-bendres.com]
Sent: Thursday, April 19, 2007 7:03 PM
To: Bobrowski, Walter

Did I miss the replies to this query somehow? Is there a technical
problem, or were the replies private? Would it be possible to post
them?

Let's not be shy (if that's it) about posting to the whole list. I've
gotten so much out of this resource (especially lately). I've had to
re-post replies to my query for others who have had the same question
and hadn't gotten the messages.

Thanks for keeping the information flowing; it's invaluable.
Jessica Cervantes
Bend Research Inc
Bend, OR

-----Original Message-----
X-from: drk-at-SHCC.org [mailto:drk-at-SHCC.org]
Sent: Wednesday, April 18, 2007 10:49 AM
To: Cervantes, Jessica

Fellow Microscopists,


A few days ago I posted a query for suggestions on how to stabilize
lysosomal membranes in cultured cells prior to immunocytochemistry. We
have
tried several of the tips but without success. Thanks to those who
replied!
We have been following the condition of the lysosomes using a GFP tag
that
we know to be specifically compartmentalized. We note that following
fixation and a rinse in TRIS-Glycine the GFP is still compartmentalized.
However, perhaps in 90% EtOH and definitely in 1:1 LR White:90% EtOH we
see
the GFP moves from the lysosomes to the cytoplasm and nucleus. It seems
that
ethanol and certainly LR White contribute to the deterioration of
membranes.
Can anyone suggest an embedding media that might be a little gentler on
membranes and still possibly work for surface label immunocytochemistry?
We
are thinking of trying Nanoplast, a water soluble media but any
suggestions
are welcome.


Thanks! Doug

Douglas R. Keene
Assistant Investigator
Micro-Imaging Center
Shriners Hospital for Children
3102 S.W. Sam Jackson Park Road
Portland, Oregon 97239
503-221-3434
drk-at-shcc.org


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From: as-at-astonmet.com
Date: Fri, 20 Apr 2007 07:42:48 -0500
Subject: [Microscopy] Re: cross section sample preparation

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Niko,

To avoid smearing, especially in the final stages
of polishing, try using Buehler's MasterMet and
MasterPrep on a spongey pad such as their
Chemocloth. This is good for flatness and
preserving delicate features even with layers of very different materials.

Alan Stone
ASTON


Note: Buehler is not the only supplier of these
products. Other metallographic suppliers may have
similar products, but I am not familiar with them.




At 04:51 AM 4/20/2007, you wrote:



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From: p.veys-at-cra.wallonie.be
Date: Fri, 20 Apr 2007 07:46:45 -0500
Subject: [Microscopy] viaWWW: Stereology : grids and methods

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Email: p.veys-at-cra.wallonie.be
Name: Pascal Veys

Title-Subject: [Filtered] Stereology : grids and methods

Question: To anyone who could be give me a tip...

We are investigating grid counting for particles counting in feed, but also taking into account their relative size : a particle being 5 times bigger than all others should be counted as 5 instead of 1). Basically we intend to use eyepiece square grids reticles. Does anyone has other proposals (eg type of grid) ? We are also looking for a good reference method description including a discussion on biases (such as that of counting only two adjacent lengths of the square...), is there an ultimate good and recent book of reference available ?

Thanks for any help.

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From: fab-at-tariffenet.it
Date: Fri, 20 Apr 2007 07:47:13 -0500
Subject: [Microscopy] viaWWW: need help fo digital camera

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Email: fab-at-tariffenet.it
Name: fabio

Organization: University of Catania

Title-Subject: [Filtered] need help fo digital camera

Question: Dear All,
I would like to mount a digital camera (such as a Canon Powershot A-540 or A-560)on my Reichert Microstar IV light microscope (equipped with a trinocular viewing body).
I know I need an adaper for the camera (LADC52F) and an adapter for the microscope trinocular body.
Which kind of adapter I need?
Any suggestions?

Thank You

Fabio
University of Catania, Italy.
fab-at-tariffenet.it






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From: oshel1pe-at-cmich.edu
Date: Fri, 20 Apr 2007 08:02:39 -0500
Subject: [Microscopy] Re: Need help with ID

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Tom,

Looks like 2 badly collapsed mite larvae. Given the scale bar on the
lower-mag shot, these are probably recently hatched. The long, fuzzy
things sticking out of the circles are sensory setae. These are
dorsal views, and the legs are the long, straight fuzzy things that
some out from underneath them. The confusing bunch of things sticking
out of the end of the one larva (whose posterior end is under the 2nd
larva) are the pedipalps and chelicerae (soft parts at this stage).
The 2 larger structures sticking "north" out of the mess are the
forelegs, and joints are just visible. No clue about the taxon, but
judging by size, I'd guess Astigmata, or whatever that group is these
days.

Mind, this could all be empty arm-waving, but I'd be willing to bet a
pitcher of good beer on it.

Phil

} Hello All,
}
} Do any of you know what this thing is? It looks like a "bug" but it's
} attached to a probable piece of fungus. Any ideas welcome, this is a head
} scratcher for everyone that has seen it.
}
} Thanks!
}
} Tom Kaye
}
} Tomkaye.com/images/fungus_lrg.jpg Long shot, the bug thing is lower right
}
}
} Tomkaye.com/images/fungus2_lrg.jpg Close up.
--
Philip Oshel
Microscopy Facility Supervisor
Biology Department
024C Brooks Hall
Central Michigan University
Mt. Pleasant, MI 48859
voice: (989) 774-3576
dept. fax: (989) 774-3462

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From: j.janssen-at-nki.nl
Date: Fri, 20 Apr 2007 08:20:59 -0500
Subject: [Microscopy] viaWWW: grids and methods

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Email: j.janssen-at-nki.nl
Name: J.W.R.M. Janssen

Organization: Dutch Cancer Institute

Title-Subject: [Filtered] grids and methods

Question: Dear Pascal,

Here is a good reference:
Recent developments for quantifying immunogold label on transmission EM thin sections Terry M Mayhew Centre for Integrated Systems Biology & Medicine, School of Biomedical Sciences, University of Nottingham, UK
Succes, Hans.

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From: JBABBITT-at-fresco.com
Date: Fri, 20 Apr 2007 10:44:44 -0500
Subject: [Microscopy] RE: Cross-sectioning packaging film

Contents Retrieved from Microscopy Listserver Archives
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I am a relative newcomer to the microscopy/histology field and need some advice on sample preparation. I am trying to section a multilayer packaging film (e.g. polyester, aluminum foil, polyethylene lamination) and am having trouble keeping the sample flat, so I can get a good reading on individual layer thicknesses. I am using a cryostat microtome for sample preparation. Is there a simple technique I can employ, or a type of embedding compound that works better for industrial applications? Thanks to any who can give me a hand, I appreciate it.

R. Jefferson Babbitt, Ph.D.
Analytical Services Manager
Fres-co System USA
3005 State Rd.
Telford, PA 18969-1021
voice - 215-721-4600 x2149
cell - 267-236-4027
fax - 215-799-8017
email - jbabbitt-at-fresco.com





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From: cervantes-at-bendres.com
Date: Fri, 20 Apr 2007 10:47:39 -0500
Subject: [Microscopy] stabilization ofmembranes

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Thanks Walter. I'm definitely interested in your protocol.

Jessica Cervantes
Bend Research Inc
Bend, OR

-----Original Message-----
X-from: Walter.Bobrowski-at-pfizer.com [mailto:Walter.Bobrowski-at-pfizer.com]
Sent: Friday, April 20, 2007 5:22 AM
To: Cervantes, Jessica

Jessica, have you attempted ICC following routine aldehyde fixation and
osmium post-fixation followed by standard epoxy embedding? The osmium
will preserve the membranes and you *may* still get successful ICC. Give
a holler and I'll send you a (work in progress) protocol that appears to
yield successful IHC on LM thick sections using RT reagents (no
microwaves, no heated steam baths).

Best regards,

Walter F. Bobrowski
Sr. Scientist
Pfizer Global R&D
2800 Plymouth Rd.
Ann Arbor, MI 48105

TEL: 734-622-7814
FAX: 734-622-5718

"The ultimate human freedom is the ability to choose one's attitude in a
given set of circumstances." -Viktor Frankl



-----Original Message-----
X-from: cervantes-at-bendres.com [mailto:cervantes-at-bendres.com]
Sent: Thursday, April 19, 2007 7:03 PM
To: Bobrowski, Walter

Did I miss the replies to this query somehow? Is there a technical
problem, or were the replies private? Would it be possible to post
them?

Let's not be shy (if that's it) about posting to the whole list. I've
gotten so much out of this resource (especially lately). I've had to
re-post replies to my query for others who have had the same question
and hadn't gotten the messages.

Thanks for keeping the information flowing; it's invaluable.
Jessica Cervantes
Bend Research Inc
Bend, OR

-----Original Message-----
X-from: drk-at-SHCC.org [mailto:drk-at-SHCC.org]
Sent: Wednesday, April 18, 2007 10:49 AM
To: Cervantes, Jessica

Fellow Microscopists,


A few days ago I posted a query for suggestions on how to stabilize
lysosomal membranes in cultured cells prior to immunocytochemistry. We
have
tried several of the tips but without success. Thanks to those who
replied!
We have been following the condition of the lysosomes using a GFP tag
that
we know to be specifically compartmentalized. We note that following
fixation and a rinse in TRIS-Glycine the GFP is still compartmentalized.
However, perhaps in 90% EtOH and definitely in 1:1 LR White:90% EtOH we
see
the GFP moves from the lysosomes to the cytoplasm and nucleus. It seems
that
ethanol and certainly LR White contribute to the deterioration of
membranes.
Can anyone suggest an embedding media that might be a little gentler on
membranes and still possibly work for surface label immunocytochemistry?
We
are thinking of trying Nanoplast, a water soluble media but any
suggestions
are welcome.


Thanks! Doug

Douglas R. Keene
Assistant Investigator
Micro-Imaging Center
Shriners Hospital for Children
3102 S.W. Sam Jackson Park Road
Portland, Oregon 97239
503-221-3434
drk-at-shcc.org


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From: walck-at-southbaytech.com
Date: Fri, 20 Apr 2007 11:18:39 -0500
Subject: [Microscopy] re: cross section sample preparation

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

I can see your problem. You have a soft material that smears with relatively hard materials and they have much different chemistries. I would like to suggest an alternative to bringing out your structure. After polishing, instead of using a chemical etch, you can use ion etching. What I would do is to ion polish at a low angle for about 10 minutes and then follow that with a high angle etch at about 35 degrees for a short time. With copper samples for light microscopy, we found that 2.5 min gave a good grain appearance at 500X and could see the interfaces with elelctroless copper layers. Since the ion polishing and etching is a physical process, it is less sensitive to the chemical nature of the materials in your cross section. We make and sell the IBS/e that can be used for this purpose and have gotten very nice results with electroplated copper samples with light microscopy. Gatan has a nicely prepared booklet that shows light microscopy results as well.

Please contact me offline and we could arrange to run some samples for you. I would only ask that we could put the results on our web site as an application note.

Disclaimer: South Bay Techonology, Inc. makes and sells the IBS/e ion beams sputter and etch system as well as metallurgical polishing equipment.

-Scott

Scott D. Walck, Ph.D.
Technical Director
South Bay Technology, Inc.
1120 Via Callejon
San Clemente, CA 92673

TEL: +1-949-492-2600
FAX: +1-949-492-1499
walck-at-southbaytech.com

-------- Original Message --------
} From: niko.hellsten-at-stratum.fi
} Sent: Friday, April 20, 2007 5:54 AM
} To: Walck-at-SouthBayTech.com
} Subject: [Microscopy] cross section sample preparation
}
} ----------------------------------------------------------------------------
} The Microscopy ListServer -- CoSponsor: The Microscopy Society of America
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} Hello everyone
}
} I'm doing basic cross section preparation for light microscopy work. My
} samples are stainless steel plated with 0-50 micrometers thick layers of
} copper and chromium.
}
} I would like to make the interfaces clearer than they are after
} grinding/polishing. I have thought about etching/corroding the surface with
} some acid or other chemical.
}
} I would like to hear from the experts what kind of chemicals they might
} recommend. Or if etching my samples chemically would do me any good at all.
}
} Thanks in advance
}
} Niko Hellstén
} Product Engineer
} Stratum Oy
} mail: niko.hellsten-at-stratum.fi
} GSM: +358-(0)440-955301
}
}
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From: cgarber-at-2spi.com
Date: Fri, 20 Apr 2007 12:20:50 -0500
Subject: [Microscopy] Preparation of multilayer packaging films

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi

I would try freezing the sample and using a single bend fracture procedure
as set out below. We have used this technique on polythene freezer bags and
many other materials for SEM but the technique is equally applicable to LM.

"Over the many years that clients and I have been investigating the cross
sections of materials by for the best method is to fracture the material.
The SEM is very clever in that it sees a cut surface and tells us "this is a
cross section cut with a sharp scalpel blade" or "this is a cross section
cut with a blunt scalpel blade" etc etc.
Preparation method A

1. Cut down the material to 1cm by 3cms place it into liquid nitrogen
until it stops bubbling.

2. Remove the material and crack it using either heavy duty tweezers or
fine pliers. If you are unable to crack the material and are forced to flex
it in order for it to crack this is not good enough! In the latter case
reduce or neck the material as shown, even a 0.5mm long crack could provide
a great deal of detail in the SEM?

3. When the pieces have dried out (condensation) they may both be
observed by LM and SEM

Fibres that will not fracture by the above method could be fractured by one
of two other methods.

Method B

1. Insert the material in a small diameter tube (thin drinking straws are
ideal). Cut the straw down to about 3cms tall. Block one end with wax,
modelling clay or similar material.

2. Using a syringe force water into the straw and block the end as above.

3. Drop the straw into liquid nitrogen then follow method A part 2 above.

4. When the pieces have dried out (condensation) they may be observed by
both LM and SEM

Method C

1. Drill 2mm to 3mm holes in a pair of stubs as shown in diagram 2.

2. Infiltrate the holes with a water soluble carbon solution and push a
bundle of fibres through the carbon solution.

3. When dry follow method A part 2 except use a blade to initiate the
crack

4. When the pieces have dried out (condensation) they may be observed by
both LM and SEM

Method C has been used with materials like freezer bags that were failing.
In this case the material was spun into a small spiral and then infiltrated
with the carbon solution."


The above data was taken from our "hints and tips" web page.

Steve Chapman
Senior Consultant Protrain
For electron microscopy consultancy and training world wide
Tel +44 1280 816512 Fax +44 1280 814007
Mobile +44 7711 606967 Web www.emcourses.com

----- Original Message -----
X-from: {JBABBITT-at-fresco.com}
To: {protrain-at-emcourses.com}
Sent: Friday, April 20, 2007 4:45 PM

R. Jefferson Babbitt, Ph.D wrote the following:
================================================================
I am a relative newcomer to the microscopy/histology field and need some
advice on sample preparation. I am trying to section a multilayer packaging
film (e.g. polyester, aluminum foil, polyethylene lamination) and am having
trouble keeping the sample flat, so I can get a good reading on individual
layer thicknesses. I am using a cryostat microtome for sample preparation.
Is there a simple technique I can employ, or a type of embedding compound
that works better for industrial applications? Thanks to any who can give
me a hand, I appreciate it.
========================================================================
We have done this same kind of system in our own laboratory. The
quick-and-dirty way to get a cross-section is liquid nitrogen fracturing
but as you point out, getting a good edge-on view is not necessarily easy.
Another danger: If you don't know in advance exactly how many layers there
are, one or more outer layers can split off further down from the fracture
surface and what you think is the fracture surface indeed might not be the
facture surface.

Hence, for SEM work, we always gold coat the two sides so that so long as we
can see in the fracture surface the two gold layers, we know we have the
entire cross-section, and in order to keep it "straight", we mount is using
an angled SEM mount (available from SPI Supplies as well as all of our major
competitors), which is then tilted 45 deg. for the head on view.

But we have pretty consistently found that a TEM view, while the sample work
up is more tedious, is far more rewarding. Most of the time one wants to
look at such films, is because there is an adhesion failure between one or
more of the layers and the TEM view is able to resolve features (such as
contaminants) between the layers or the dispersion of inorganic fillers in
one or more of the layers. We still gold coat such films (with passivation
layers) before embedding to ensure that there is not interaction of the
embedding resin with the polymer film layers. Our preferred embedding resin
is our own SPI-Pon 812 epoxy- based embedding resin (but we believe
equivalent results will be obtained with the equivalent sold by others).

One other thing: The cross-sectioning, irrespective of what method you are
using, must be done cryo, with an ultramicrotome using a diamond knife. A
glass knife will not last very long against the aluminum foil layer.

Since you are a "neighbor" to SPI Supplies, we would be happy to have you
visit and we would show you how we do these kinds of films.

Disclaimers: Mentioned in this posting are some of our own products and we
have the vested interest in promoting their use.

Chuck

===================================================
Charles A. Garber, Ph. D. Ph: 1-(610)-436-5400
President
SPI SUPPLIES FAX: 1-(610)-436-5755
PO BOX 656 e-mail: cgarber-at-2spi.com
West Chester, PA 19381-0656 USA Cust. Service: spi2spi-at-2spi.com


Look for us!
############################
WWW: http://www.2spi.com
############################
==================================================




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From: drk-at-SHCC.org
Date: Fri, 20 Apr 2007 12:36:52 -0500
Subject: [Microscopy] responses to membrane stabilization querry (long)

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Fellow Microscopists:

Many thanks to those who responded to my request for suggestions for
stabilizing membranes (lysosomes in particular). My specific aim in this
experiment is to stabilize cultured cells containing GFP tagged lysosomes
for surface-label immunocytochemistry with the hope of co-localizing GFP
expressing protein (using confocal images overlaid onto TEM images cut from
the next serial section) and another potentially interactive protein
localized with immunogold on the TEM section. We are able to follow GFP
emission through the protocol using our confocal microscope. In cultures
fixed in media buffered 4% paraformaldehyde/1% glutaraldehyde, we see that
GFP remains compartmentalized up to 90% ethanol but after the introduction
of 1:1 90% EtOH:LRWhite, GFP is no longer compartmentalized and instead is
distributed throughout the cytoplasm and nucleus. I am now in the process
of trying some of the ideas. A preliminary result suggests that the
lysosomes are stabilized somewhat more by the inclusion of 4% picric acid;
also by progressively lowering temperature during graded ethanol dehydration
to minus 20C, embedding in Lowicryl HM20 at -20C, and polymerization at
-20C. We have yet to section the HM20, but we hope that confocal microscopy
on 0.5um sectioned HM20 will reveal compartmentalized GFP. Then we'll see
what mess we've made of the additional antibody-binding epitopes. We love a
challenge!

To address the request that the responses be shared, here is a summary.
Since some of these responses were made privately, I have not included the
author's names.

Response #1:

what may help: high-pressure immobilization (cryo-fixation; expensive but
really good),
followed by freeze-substitution at -90 (8 to 48 hrs)/-60 (8hrs)/-30 (6 to 8
hrs) as described in several papers.

It is worth trying:
Aceton + 0.1/0.2% OsO4, +0.5% Uac +/-GA (0.1 to 1%) +/-FA (0.25 to 2%)
(MANY variants possible, I know)
or
EtOH, no OsO4, but add some or all other chemicals/fixatives
MeOH, no OsO4, but add some or all ...
Aceton + 2%GA (ready available as it is)
Aceton + 0.2%GA + UAc 0.5% ...
and so on.

The advantage of cryo-substitution at very low temperatures:
The chemicals are not reactive at low temperature initially (only slowly at
-60, and then at higher temperatures). The chemicals become evenly
distributed in the cell/tissue, and then react at the same time upon
warming, everywhere, similarly. Result: tissue, cells and membranes are
often better preserved. in addition, you may add some water (1 - 5%?) to the
freeze-substitution medium, (YES!!), as suggested by Paul Walther a few
years ago.
We have done this, others as well, with success.

Response #2:

Have you tried tannic acid! It is supposed to stabilize plasma membranes,
don't know about Lysosomal membranes,

Response #3"

While it would involve doing freeze-substitution, Lowicryl HM 20
is great for membranes. You would need to do low temperature dehydration
after room temperature or 4 degree C aldehyde fixation. I used to use a
small amount of glutaraldehyde with the methanol free buffered formalin. I
also used uranyl acetate to help preserve membranes and dehydrated cold with
methanol. You can look at my paper for details:

The Journal of Histochemistry and Cytochemistry 40(10):1491-1500, 1992
"Immunocytochemical Localization of Lysozyme and Surfactant Protein A in Rat
Type II Cells and Extracellular Surfactant"

Response #4:

I have a couple of thoughts on the problem. I don't think you are getting
any buffering capacity from the culture medium. And if there is any serum
in the medium, you have titrated all the aldehydes with the serum and have
no functional fixative left when you are trying to fix the cells.

Summary of additional responses:

These included longer fixation times, fixation at ambient temperature not
4C, and the importance of including Calcium in the fixation buffer.

Again, thank you to those who responded and to all interested microscopists!

Doug Keene
Douglas R. Keene
Assistant Investigator
Micro-Imaging Center
Shriners Hospital for Children
3102 S.W. Sam Jackson Park Road
Portland, Oregon 97239
503-221-3434
drk-at-shcc.org


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From: gerard.cox-at-goodrich.com
Date: Fri, 20 Apr 2007 12:48:07 -0500
Subject: [Microscopy] New SEM Purchase

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Our group wants to buy a new SEM to replace an old AMRAY machine for failure analysis and quality control investigations. We also need EDS capabilities, and do not anticipate the need for any other analysis tools. It seems like we will need to go to 10 000X only or thereabouts, and we would like to have low vacuum capabilities for imaging nonmetallic components / painted parts. We want a large chamber, and a large range of stage motion (100 mm X 80 mm X 80 mm min.) We need the new machine to last a really long time, be easily maintained, and spare parts should be available for the indefinite future, as I do not anticipate funding for anything like this again for over a decade. I think that analog imaging is preferred to digital acquisition because of alleged "software fudging" in the latter (or something.)

We are looking at a JEOL JSM-6490LV and a Hitachi S-3400N specifically, (my manager's choices) and I have seen a CamScan and a few FEI models. My initial impressions are that the CamScan unit is a bit specialized and that the service/support won't be as effective (we are in southern Ontario) and that the FEI machines will be WAY too expensive and more tailored to bio applications / really high-end research. As to the JEOL and Hitachi, I was told the JEOL is slightly better and the company is less likely to disappear (ie, better support and spare parts in the long-term) while the service and support for the Hitachi people is superior, both initially and long-term.

I realize I am asking a great deal, and would appreciate any input into this matter. Has anyone bought or used either of the models listed above? Does anyone have any comments on what we do or do not want? Is Peltier cooling instead of LN2 really a good idea? Any input as to EDS machines and software to buy or to avoid? Thanks for your help.

Gerard Cox


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From: kraftpiano-at-gmail.com
Date: Fri, 20 Apr 2007 15:10:08 -0500
Subject: [Microscopy] SEM: Replacing diffusion pump water cycle with coolant.

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Just a brief question to the list: I've been working on the cooling
system to my JSM-840 when an idea struck me. I am having problems
because the water pump that I have to circulate the chilled water is
not powerful enough to produce the pressure needed to circulate water
through the SEMs diffusion pumps. The pump is actually rated for a
coolant, though (Antifreeze/DI Water mixture) and I was wondering
what you guys think about instead of using water to chill the
diffusion pumps and amplifier electronics, using some form of coolant
with a lower viscosity than water, which would alleviate my need for
such high pressures and let me use the pump that fits the chiller I
have.

--Justin A. Kraft

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From: TJJ-at-stowers-institute.org
Date: Fri, 20 Apr 2007 16:04:09 -0500
Subject: [Microscopy] Recommended humidity level

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Can anybody give me an optimal % relative humidity that is recommended
for EM rooms? We recently had some failures with formvar grids (we
think) due to excessive room humidity when they were being made. I can
bring in a de-humidifier, but what would be considered to be optimal?

Teri Johnson, HT(ASCP)QIHC
Managing Director Histology Facility
Stowers Institute for Medical Research
1000 E. 50th St.
Kansas City, MO 64110



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From: gary-at-gaugler.com
Date: Fri, 20 Apr 2007 16:36:17 -0500
Subject: [Microscopy] Re: SEM: Replacing diffusion pump water cycle

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

You did not say what brand chiller you have.
What flow rate and pressure do you need? For
just a diffusion pump (no electronics), I don't think a huge
rate is needed. I think you need to set the temperature
and have the correct flow rate rather than
concentrate on pressure. If you can't get the
rate, then that is what you should focus on,
IMO.

Haskris and probably others specifically say
to NOT use anti-freeze. Some folks survive
very well just using distilled water. That
has not been my experience. I find that 10%
mix of 100% Ethylene Glycol and DI works great. Most
chillers use really cheap brass fittings rather
than Imperial brass. Consequently, a bad mix
of coolant will cause corrosion and also lead to
algae growth. The other gotcha are the hoses.
Use opaque ones rather than transparent ones.
Keeping the light out inhibits algae growth too.

In my Haskris R50 chiller with 5 gallon reservoir,
water or the mix results in the same pressure
at same flow rate. What will cause pressure to
change is a dirty tank filter, or especially the
external toilet paper filter (50u fiber mesh).

gary g.



At 12:12 PM 4/20/2007, you wrote:

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From: drk-at-SHCC.org
Date: Fri, 20 Apr 2007 16:36:45 -0500
Subject: [Microscopy] Recommended humidity level

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hello Teri,

If it is for formvar that you wish to keep humidity low, you might consider
casting your formvar films within a glove bag flushed with dry nitrogen gas.
We use such a system here in our Oregon lab with good success. The bags we
use are from I2R and the web address is:
http://www.i-2-r.com/glove_bag/l_glove_bags/p_x_r/x_r.htm. I have no
financial interest.

Doug

Douglas R. Keene
Assistant Investigator
Micro-Imaging Center
Shriners Hospital for Children
3102 S.W. Sam Jackson Park Road
Portland, Oregon 97239
503-221-3434
drk-at-shcc.org

-----Original Message-----
X-from: TJJ-at-stowers-institute.org [mailto:TJJ-at-stowers-institute.org]
Sent: Friday, April 20, 2007 2:08 PM
To: drk-at-SHCC.org

Can anybody give me an optimal % relative humidity that is recommended
for EM rooms? We recently had some failures with formvar grids (we
think) due to excessive room humidity when they were being made. I can
bring in a de-humidifier, but what would be considered to be optimal?

Teri Johnson, HT(ASCP)QIHC
Managing Director Histology Facility
Stowers Institute for Medical Research
1000 E. 50th St.
Kansas City, MO 64110



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From: ejb1176-at-gmail.com
Date: Fri, 20 Apr 2007 16:44:11 -0500
Subject: [Microscopy] Re: SEM: Replacing diffusion pump water cycle with

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi Justin,
Does JEOL list a spec, for the flow rate? Too much may give you
excess vibration.

Could the lines/pump have some blockage?

Restricting the outlet, a little, will increase the backpressure, it
might be enough to trip the interlock, if that's shutting things off.

I've added up to 5% ETHYLENE GLYCOL to recirculating cooling systems
(EBEAM and SEM and TEM) with no long-term deleterious effects. Not
sure how much that will change the viscosity.

I've always been advised against running DI water alone as it is ion
hungry and may leach metal pipes. I've always used grocery store
distilled water.

Best of Luck.

Ed Basgall, PhD
Irvine, CA 92612

email: ejb1176-at-gmail.com


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From: tivol-at-caltech.edu
Date: Fri, 20 Apr 2007 17:19:30 -0500
Subject: [Microscopy] Re: Recommended humidity level

Contents Retrieved from Microscopy Listserver Archives
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On Apr 20, 2007, at 2:04 PM, TJJ-at-stowers-institute.org wrote:

} Can anybody give me an optimal % relative humidity that is recommended
} for EM rooms? We recently had some failures with formvar grids (we
} think) due to excessive room humidity when they were being made. I can
} bring in a de-humidifier, but what would be considered to be optimal?
}
Dear Teri,
You need not only to be concerned about the formvar, but you also do
not want condensation on the column or electronics. Too low a humidity
will also allow the generation of static electricity. About 40% RH is
a very good value, and the maximum permissible depends on the
difference in temperature between the room and the scope and is usually
about 60%.
Yours,
Bill Tivol, PhD
EM Scientist
Electron Cryo-Microscopy Facility
Broad Center, Mail Code 114-96
California Institute of Technology
Pasadena CA 91125
(626) 395-8833
tivol-at-caltech.edu


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From: kraftpiano-at-gmail.com
Date: Fri, 20 Apr 2007 17:43:12 -0500
Subject: [Microscopy] Re: SEM: Replacing diffusion pump water cycle with coolant.

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Sorry, I wasn't very clear about the chiller before. It's not a name
brand chiller- it's actually a part from a larger system, but I don't
know what that larger system is- I bought it locally as industrial
surplus. Here's what I know about the recirculator system:

Pump: Iwaki Magnetic drive pump. 12 L/min. Max. head 2.1m.

There is a heat exchanger unit and all of the condenser piping
necessary to chill the water, and it can divide the output a maximum
of three ways, so I can have the electronics set on a different water
circuit than the diffusion pumps. When I say that the pressure is not
enough to push the water through, I mean that the pump pumps, but very
little water is pushed through, and it is shutting down because of
thermal overload. I know that the JEOL manual specifies 5 L/min. at
12-36 PSI, but I'm not sure how that translates from "Max head" to
PSI. The pump's flow rate is more than enough to handle it, but it
isn't making it through. That's why I was thinking about lower
viscosity fluids, which should flush through at a higher flow rate and
a lower PSI.

--Justin.

On 4/20/07, kraftpiano-at-gmail.com {kraftpiano-at-gmail.com} wrote:
}
}
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} Just a brief question to the list: I've been working on the cooling
} system to my JSM-840 when an idea struck me. I am having problems
} because the water pump that I have to circulate the chilled water is
} not powerful enough to produce the pressure needed to circulate water
} through the SEMs diffusion pumps. The pump is actually rated for a
} coolant, though (Antifreeze/DI Water mixture) and I was wondering
} what you guys think about instead of using water to chill the
} diffusion pumps and amplifier electronics, using some form of coolant
} with a lower viscosity than water, which would alleviate my need for
} such high pressures and let me use the pump that fits the chiller I
} have.
}
} --Justin A. Kraft
}
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From: vitalylazar-at-att.net
Date: Fri, 20 Apr 2007 18:05:05 -0500
Subject: [Microscopy] Re: SEM: Replacing diffusion pump water cycle

Contents Retrieved from Microscopy Listserver Archives
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ditto that- 30 psi is enough, unless cooling system is clogged. If it is
clogged, then concentrate your efforts on unclogging the cooling system,
rather than increasing pressure. The highest water pressure that I can
imagine being required for any SEM/TEM is in mid-40 psi. I typically set
much lesser pressure, between 25 and 35 psi. Compensating poor flow in a
clogged system with higher pressure is a bad habit. Plus, high pressure
erodes rubber and plastic components of the cooling system, and that alone
accelerates formation of clogs. Especially with old instrument.

I suggest to have at least 1 flowmeter with flow control (it is cheap). And
pressure reducer with bypass line for the water pump - every decent chiller
has that anyway. Pump itself shall be capable of at least 100 psi. Not for
everyday operation, but for troubleshooting, especially if you have old
instrument. You can easily detect presence of a clog (if not location...),
by adjusting and monitoring pressure and flow rate. More than one flowmeter
is good to have if cooling system has parallel branches.

Likely places for clogs in JEOL-840 are: quick connections, lower (hottest)
water line coils on both ODPs, and of course filters if any are present.
Less likely places are electronics and obj. lens. But this is never certain.

To remove clog, reverse the direction of water flow, or use small amount
water with compressed air in reversed direction. But first disconnect
various parts of cooling circuit, and determine where the clog is located.
If you reverse the whole thing at once, clog might get worse and harder to
remove. You will need a variety of hoses and fittings to do this work
efficiently.

Flow rates at room T~20C and water T~17C: 1gpm is great, 0.5gpm is OK, 0.2
gpm is critically low, below that expect thermal protection to trip at any
moment.

Vitaly Feingold
SIA
2773 Heath Lane
Duluth GA 30096
Ph. 770-232-7785
Fax 770-232-1791
www.sia-cam.com
----- Original Message -----
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To: {vitalylazar-at-att.net}
Sent: Friday, April 20, 2007 5:37 PM


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From: hanke-at-mee-inc.com
Date: Fri, 20 Apr 2007 18:42:58 -0500
Subject: [Microscopy] Re: cross section sample preparation

Contents Retrieved from Microscopy Listserver Archives
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Fracture method will not work on this sample. Stainless steel and copper
are very ductile and will bend and neck down before breaking. These
metals are not made brittle by cold temperatures.

Sample preparation, i.e. good polishing methods is the key to this
evaluation. This combination can be polished mechanically, but a good
procedure and technique will be required.

--
Larry D. Hanke, P.E.
Materials Evaluation and Engineering, Inc.
Practical Solutions Through Technology and Innovation
http://www.mee-inc.com (763) 449-8870


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From: gary-at-gaugler.com
Date: Fri, 20 Apr 2007 20:49:45 -0500
Subject: [Microscopy] Re: 2nd for posting to the list

Contents Retrieved from Microscopy Listserver Archives
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The reason NOT to post to the list is that you get
volumes of "Out Of Office" messages. This is the
same as when you make a new posting. Most of the
defunct messages are trapped by Eudora but quite
a few still get though....sigh.

Some do not have this subject but say that they
are gone from xx to yy.

gary g.



At 03:50 PM 4/19/2007, you wrote:
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From: W.Muss-at-salk.at
Date: Sat, 21 Apr 2007 06:14:22 -0500
Subject: [Microscopy] Re:AskAMicroscopist: negative staining whith a small lipo protein

Contents Retrieved from Microscopy Listserver Archives
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Dear Alvaro,
interesting question....
Normally (e.g. as I use it sometimes for negative staining of virus particles)
you will have at least two negative staining solutions:
i) hydrous PTA (1, 2 or other percentage)
ii) hydrous uranylacetate 1-4%.......
for (small) lipoproteins (esp. for HDL-like) I am not quite sure wether simple
saying so or giving advice in that way is helpful.

As I understand negative staing, also (a) positive result(s)will depend on pH
(and therefore [with what ingredients] buffering the solution eventually to
which "special" pH), and (absorption/adhesion) technique of specimen
preparation.
I don't think your carbon-coated formvar-filmed copper grids are a
problem....but,. if I remember correctly, there are several (also older)
papers/articles on negative staining techniques for e.g. liposomes (for an
imagination on such try search phrase } } "negative staining","liporotein"
{ {) reporting some very specific caudeles for adhesion of lipoprotein
material....(for instance: see*) below)
Some prefer also prefixation of mixed particles with hydrous Osmium tetroxide
before negative staining with the heavy metal solution, sometimes only hydrous,
somtetimes with an additive (like sucrose).....
so it may depend also on the type of material you'd like to have demonstrated
and wether you are able to get the (macro-)molecule adhering in a stabilized
form to the formvar-carbon-surface of the grid or not (cf. *)

Once determined [by trial&error (perhaps, unluckily)] how to proceed with the
grids' properties = hydrophilization and immediate use or storage for
months...see *), adhesion time/technique, eventually prestabilization of the
specimen by additional fixation, the right negative staining solution (also in
terms of i) element [PTA, UO2, AmmMolybdat,Uranylformate, etc.],
ii)concentration, iii) pH of the solution, iv) specific additives necessary?)
the technique itself yields reliable and rapid rsults, even within 5-10 minutes
(as I have read in some papers) ==} that's what I would like to wish you in
overcoming your problem.


Best regards
Wolfgang Muss, Salzburg, AUSTRIA

cf:
*) Original paper in:
J Lipid Res. 1980 Nov;21(8):981-92.
Unilamellar liposomes made with the French pressure cell: a simple preparative
and semiquantitative technique.
Hamilton RL Jr, Goerke J, Guo LS, Williams MC,Havel RJ.
Ex Material & Methods-section:
Negative staining of liposomes often causes artifactual images resulting from
disruption of small liposomes that subsequently form larger multilamellar
structures. Although the mechanism of this process is not understood, it may be
caused in part by the intense hydrophobicity of freshly evaporated carbon on
grid surfaces. Our attempts to modify the surface film of freshly prepared
carbon-coated grids (200-300 mesh copper grids, Fullum, Schenectady,NY) by glow
discharge, polylysine, or addition of albumin to sample or grid did not prove
satisfactory. However, we have learned empirically that parlodioncovered
grids with carbon films made with a Siemens evaporator (VI3 G 500) permit even
spreading of liposomes without apparent structural changes, provided that the
grids have been aged 6- 12 months on the shelf. Carbon rods for filming were
obtained from Ringsdorff-Herke (Spektral Kohlen, Bonn-Bad Godesberg, West
Germany). With such “matured” carbon-coated grids, liposomes were prepared for
electron microscopy with 2% potassium phosphotungstate at pH 6.45-6.5 by the
drop procedure described previously (1 1). We found that the lipid
concentration in the sample was also important for preparing uniform spreads.
Optimal results were more consistently obtained with samples containing
1- 10 mg/ml PC. Improved results can be obtained for more dilute samples by
increasing contact time of the sample on the grid to 2-3 min, and by using
a tighter 400 mesh grid.......



Zitat von alvarobq-at-fcien.edu.uy:

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} Below is the result of your feedback form (NJZFM-ultra-55). It was submitted
} by (alvarobq-at-fcien.edu.uy) from
} http://www.microscopy.com/Ask-A-Microscopist/Ask-A-Microscopist.html on
} Friday, September 15, 2006 at 08:40:57
} ---------------------------------------------------------------------------
}
} Email: alvarobq-at-fcien.edu.uy
} Name: Alvaro D. Olivera
}
} Organization: Science University
}
} Education: Undergraduate College
}
} Location: Montevideo - Uruguay
}
} Question:
}
} I'm TEM technician and advanced undergraduate in Biochemistry.
} I'm trying negative staining whith a small lipo protein HDL like. I'm
} using CARBON-FORMVAR COATED Cu GRIDS and PTA 2% and 3%. I can't see it.
} What do you suggest?
}
} Many thanks, Alvaro.
}
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From: randerson20-at-tampabay.rr.com
Date: Sat, 21 Apr 2007 06:36:33 -0500
Subject: [Microscopy] 2nd for posting to the list

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hmmm. I get maybe 3 or 6 out of office msgs/post.

Ron

gary-at-gaugler.com wrote:
} ----------------------------------------------------------------------------
} The Microscopy ListServer -- CoSponsor: The Microscopy Society of America
} To Subscribe/Unsubscribe -- http://www.microscopy.com/MicroscopyListserver
} On-Line Help http://www.microscopy.com/MicroscopyListserver/FAQ.html
} ----------------------------------------------------------------------------
}
} The reason NOT to post to the list is that you get
} volumes of "Out Of Office" messages. This is the
} same as when you make a new posting. Most of the
} defunct messages are trapped by Eudora but quite
} a few still get though....sigh.
}
} Some do not have this subject but say that they
} are gone from xx to yy.
}
} gary g.
}
}
}
} At 03:50 PM 4/19/2007, you wrote:
}
} } ----------------------------------------------------------------------------
} } The Microscopy ListServer -- CoSponsor: The Microscopy Society of America
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} } ----------------------------------------------------------------------------
} }
} }
} } I would like to 2nd the idea that replying to the list is a good thing. This
} } is my only resource for such information so I would rather delete than miss
} } an opportunity to learn something.
} }
} } Thanks!
} }
} } Tom Kaye
} }
} } Not affiliated with anything.
} }
} } -----Original Message-----
} } X-from: cervantes-at-bendres.com [mailto:cervantes-at-bendres.com]
} } Sent: Thursday, April 19, 2007 6:02 PM
} } To: tom-at-tomkaye.com
} } Subject: [Microscopy] RE: stabilization of membranes
} }
} }
} }
} } ----------------------------------------------------------------------------
} } The Microscopy ListServer -- CoSponsor: The Microscopy Society of America
} } To Subscribe/Unsubscribe -- http://www.microscopy.com/MicroscopyListserver
} } On-Line Help http://www.microscopy.com/MicroscopyListserver/FAQ.html
} } ----------------------------------------------------------------------------
} }
} } Did I miss the replies to this query somehow? Is there a technical
} } problem, or were the replies private? Would it be possible to post
} } them?
} }
} } Let's not be shy (if that's it) about posting to the whole list. I've
} } gotten so much out of this resource (especially lately). I've had to
} } re-post replies to my query for others who have had the same question
} } and hadn't gotten the messages.
} }
} } Thanks for keeping the information flowing; it's invaluable.
} } Jessica Cervantes
} } Bend Research Inc
} } Bend, OR
} }
} } -----Original Message-----
} } X-from: drk-at-SHCC.org [mailto:drk-at-SHCC.org]
} } Sent: Wednesday, April 18, 2007 10:49 AM
} } To: Cervantes, Jessica
} } Subject: [Microscopy] stabilization ofmembranes
} }
} } ------------------------------------------------------------------------
} } ----
} } The Microscopy ListServer -- CoSponsor: The Microscopy Society of
} } America
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} } http://www.microscopy.com/MicroscopyListserver
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} } ----
} }
} } Fellow Microscopists,
} }
} }
} } A few days ago I posted a query for suggestions on how to stabilize
} } lysosomal membranes in cultured cells prior to immunocytochemistry. We
} } have
} } tried several of the tips but without success. Thanks to those who
} } replied!
} } We have been following the condition of the lysosomes using a GFP tag
} } that
} } we know to be specifically compartmentalized. We note that following
} } fixation and a rinse in TRIS-Glycine the GFP is still compartmentalized.
} } However, perhaps in 90% EtOH and definitely in 1:1 LR White:90% EtOH we
} } see
} } the GFP moves from the lysosomes to the cytoplasm and nucleus. It seems
} } that
} } ethanol and certainly LR White contribute to the deterioration of
} } membranes.
} } Can anyone suggest an embedding media that might be a little gentler on
} } membranes and still possibly work for surface label immunocytochemistry?
} } We
} } are thinking of trying Nanoplast, a water soluble media but any
} } suggestions
} } are welcome.
} }
} }
} } Thanks! Doug
} }
} } Douglas R. Keene
} } Assistant Investigator
} } Micro-Imaging Center
} } Shriners Hospital for Children
} } 3102 S.W. Sam Jackson Park Road
} } Portland, Oregon 97239
} } 503-221-3434
} } drk-at-shcc.org
} }
} }
} } ==============================Original
} } Headers==============================
} } 7, 22 -- From drk-at-SHCC.org Wed Apr 18 12:43:18 2007
} } 7, 22 -- Received: from mail.SHCC.org (mail.shcc.org [64.213.211.202])
} } 7, 22 -- by ns.microscopy.com (8.12.11.20060308/8.12.8) with
} } ESMTP id l3IHhITP002098
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} } 12:43:18 -0500
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} } Microscopy-at-Microscopy.Com;
} } 7, 22 -- Wed, 18 Apr 2007 10:41:57 -0700 (PDT)
} } 7, 22 -- Date: Wed, 18 Apr 2007 10:43:58 -0700
} } 7, 22 -- From: Doug Keene {drk-at-SHCC.org}
} } 7, 22 -- Subject: stabilization ofmembranes
} } 7, 22 -- Sender: drk-at-SHCC.org
} } 7, 22 -- To: Microscopy-at-Microscopy.Com
} } 7, 22 -- Cc: drk-at-SHCC.org
} } 7, 22 -- Reply-to: drk-at-SHCC.org
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} }
} }
} } ==============================Original Headers==============================
} } 13, 16 -- From cervantes-at-bendres.com Thu Apr 19 17:57:57 2007
} } 13, 16 -- Received: from BRIEX04A.bri.local (bc161112.bendcable.com
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} } 13, 16 -- MIME-Version: 1.0
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} } 13, 16 -- charset="us-ascii"
} } 13, 16 -- Subject: RE: [Microscopy] stabilization of membranes
} } 13, 16 -- Date: Thu, 19 Apr 2007 15:57:55 -0700
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} } 13, 16 -- In-Reply-To: {200704181748.l3IHmsrE012175-at-ns.microscopy.com}
} } 13, 16 -- References: {200704181748.l3IHmsrE012175-at-ns.microscopy.com}
} } 13, 16 -- From: "Cervantes, Jessica" {cervantes-at-bendres.com}
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} }
} } ==============================Original Headers==============================
} } 25, 20 -- From tom-at-tomkaye.com Thu Apr 19 18:47:51 2007
} } 25, 20 -- Received: from tomkaye.com (mxgateway.techpro.com [64.4.207.8])
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} } tomkaye.com with ESMTP
} } 25, 20 -- (SMTPD32-8.14) id AFAD3312012A; Thu, 19 Apr 2007 18:47:57 -0500
} } 25, 20 -- From: "Tom Kaye" {tom-at-tomkaye.com}
} } 25, 20 -- To: {microscopy-at-microscopy.com}
} } 25, 20 -- Subject: 2nd for posting to the list
} } 25, 20 -- Date: Thu, 19 Apr 2007 18:48:03 -0500
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} } ==============================End of - Headers==============================
} }
}
}
} ==============================Original Headers==============================
} 7, 20 -- From gary-at-gaugler.com Fri Apr 20 20:49:45 2007
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} 7, 20 -- Date: Fri, 20 Apr 2007 18:49:48 -0800
} 7, 20 -- To: tom-at-tomkaye.com
} 7, 20 -- From: Gary Gaugler {gary-at-gaugler.com}
} 7, 20 -- Subject: Re: [Microscopy] 2nd for posting to the list
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==============================Original Headers==============================
4, 19 -- From randerson20-at-tampabay.rr.com Sat Apr 21 06:36:32 2007
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4, 19 -- Date: Sat, 21 Apr 2007 07:36:28 -0400
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From: zaluzec-at-microscopy.com
Date: Sat, 21 Apr 2007 08:25:22 -0500
Subject: [Microscopy] Out of Office messages & posting comments to the list

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Colleagues.....

Replying to the list is not only appropriate, but should be done in almost
all cases. The obvious exception I could see is when a private reply
is appropriate, or a vendor is discussing a reply to a query with detailed
product information about a commerical item to an individuals request.

Remember the primary purpose of this list is to share our communal
expertise, if you post messages privately then this knowledge distribution
is curtailed. Of course, some people post summaries of replies
to their questions. This is a good procedure, and is also suggested
in the FAQ, and I would encourage people who receive alot of private replies to do this
as a courtesy to the community. Consider it part of the way you
pay the astronomical annual fees charged to each of you for being
a member of this forum.

FYI, there is nothing I can do to stop "out of the office" type replies, since
those come from the individuals and never pass through the listserver
filters. If you read the Listserver FAQ, I request that if you are unavailable
then you should unsubscribe from the list and then resubscribe when
you return. There are alot of people that do this (THANK YOU), but
obviously some do not.

In principle you won't miss anything, if you unsubscribe for a short while,
as all the messages are archived, however, there are clearly people who
choose not to follow this request for various reasons.

An alternative should you be wary of missing something, or if
your company policy requires you to use Out of the Office messages, would
be to have 2 addresses. One for your official mail (to which you could
add the Out of the Office reply), while a second which is only used for
Listserver traffic. This would be the logical approach for those
subscribers who use the Out of the Office message frequently.

As Gary G. mentioned most Email programs today allow you
to filter mail by topic, and I certainly, also use this mechanism to
refine the distribution of all Emails I personally get into appropriate folders.
If you do this then the issue becomes relatively minor, considering
the proponderance of SPAM/JUNK mail.

If it is not obvious to you by now all Listserver Email has the
following text in the subject line
[Microscopy]
that was done in order to allow you to create a filter
to put all listserver Email into a folder.

Fortunately for all of you the primary filters on the subscription
lists now catch nearly all of the junk/spam mail which is sent
to "microscopy-at-". For the record, long ago spam exceeded 500
messages/day, which I filter out for you. So a few ocassional
out of the office replies is a small price to pay for the information you
get for subscribing to this forum.

Cheers,


Nestor
Your Friendly Neighborhood SysOp.

==============================Original Headers==============================
12, 13 -- From zaluzec-at-microscopy.com Sat Apr 21 08:25:22 2007
12, 13 -- Received: from [206.69.208.22] (mac22.zaluzec.com [206.69.208.22])
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12, 13 -- References: {200704211136.l3LBaXsH031128-at-ns.microscopy.com}
12, 13 -- Date: Sat, 21 Apr 2007 08:25:18 -0500
12, 13 -- To: microscopy-at-microscopy.com
12, 13 -- From: "Nestor J. Zaluzec" {zaluzec-at-microscopy.com}
12, 13 -- Subject: Out of Office messages & posting comments to the list
12, 13 -- Content-Type: text/plain; charset="us-ascii"
==============================End of - Headers==============================




From: keith.morris-at-ucl.ac.uk
Date: Sat, 21 Apr 2007 09:12:21 -0500
Subject: [Microscopy] AskAMicroscopist: count gold particles

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Dear Alida,

Software image analysis of TEM film or digital images isn't always easy as
it is often difficult for the software to distinguish the objects you wish
to count from the rest of the image. However our brains can generally do a
far better job in picking out (discriminating) what we want to count or
measure. But you have be careful with things like sampling procedure and
image quality to make sure you don't bias the results.

Generally, even with modern computers, it is often quicker to count by eye
than get software to do this for you. This is particularly so if there are
only a few objects (less than 50) in the image. However if you can easily
software threshold (detect) the objects you wish to count then the software
can count them automatically very quickly. But often the 'detected'
thresholded binary overlay will need editing to remove false objects, and
this may take far longer than simply counting by eye.

In most cases careful preparation of the specimen and optimising image
capture and microscope optics will be essential to produce images are most
suited to semi-automatic image analysis software. For example if you wish to
count cells under optical microscopy, plate them at lower densities so that
they will not overlay each or frequently touch and so can be easily
separated and counted by software algorithms. Things like blue DAPI
fluorescence staining of the nucleus will enable cell numbers to be counted
very quickly semi-automatically, although it will get into trouble if a lot
of cells are multi-nuclear or in different focus planes. Often though, even
if the software doesn't automatically count the objects as 'accurately' as
we can by eye, the biological variation across samples is far higher than
these counting errors. Indeed different users will invariably produce
different counts for the same samples.

If, as is often the case with TEM and optical phase contrast transmission
images, it is very difficult to only threshold the objects of interest, then
manual counting is generally the quickest option. Image analysis software
can still help here though. Biomedical image analysis programs like
MetaMorph (http://www.moleculardevices.com/pages/software/metamorph.html)
have applications that allow you to simply click on each object with the
mouse to count them. The screen then marks the point with a coloured number
(so you can see you have counted it) and it automatically adds up all the
objects you have clicked on in the image. You can give different types of
objects different coloured markers, so that the count totals go into
different bins (up to eight different objects types in one go). Once
completed the count data can then be logged to an Excel spreadsheet or noted
down.

However MetaMorph image analysis software costs several thousand pounds. On
the plus side it can do far more than just manually count (which we are very
good at with our object discriminating brain), for example it can also
measure length, area and perimeter, track cell movement or estimate
co-localisation (which we are far less successful at, even with some sort of
reference aid onscreen, e.g. length micrometers or circles of known area).

However you get pretty good PC based image analysis software for free, in
the shape of open-source 'ImageJ' image analysis software, see
http://rsb.info.nih.gov/ij (or its sister program NIHImage for the apple
http://rsb.info.nih.gov/nih-image).

Having many Metamorph licences I have never used ImageJ to count objects,
but it has all the standard thresholding (object detection) and image
analysis routines (e.g. area, perimeter, length/distance, pixel
intensity/brightness). ImageJ can be further expanded by a list of plug-ins
written by devoted users (these are just copied to the ImageJ plug-in folder
and will then appear in the ImageJ menu, spookily under the word 'Plugins').


ImageJ even has a plug-in that is the exact equivalent of Metamorph's manual
count application (See plug-in 'CELL COUNTER'), and it works in a very
similar fashion to MetaMorphs version (and for free). You can also simply
use a program like Photoshop or even Paint to put a little blob of colour
over each object to be counted (destroying the original image so ensure you
have a backup). You can then easily threshold and count the blobs with
ImageJ (but using plug-in CELL COUNTER is naturally far easier for just
counting, colouring in the objects is more useful for things like object
area). This Cell Counter software works just like putting a clear plastic
sheet over the VDU screen and marking off the objects with a felt pen (and
ImageJ counts them for you as well). The software can actually mark the
original image so that the counts get scored into it or the count marks
marks can be left on an 'overlay' with the original image unchanged (with no
record of which objects were counted when the image is next viewed).

These manual count software routines prevent double counting errors and
simply forgetting what number you got to (in the old days you used a
mechanical one-hand click counter). Like MetaMorph, ImageJ can do an awful
lot more image analysis than just manual count. It will always be useful to
have an image editing software package like Photoshop at hand as well. Plus
a cheap Wacom graphics tablet can be advantageous for some things (like
drawing round objects etc..), used in combination with the PC mouse, see
www.Wacom.com

If you only have TEM negatives, simply scan them into PC digital form using
a cheap flat bed large format (A4) film scanner like the Epson 4990 Photo
(£250). ImageJ is happy with standard digital images, e.g. jpg and tif
formats.

If you need any more info/help, just ask.

Regards

Keith

---------------------------
Dr Keith J Morris
Imaging Facilities Manager
Cell Biology
Institute of Ophthalmology
UCL, London EC1V 9EL






-----Original Message-----
X-from: akoorts-at-medic.up.ac.za [mailto:akoorts-at-medic.up.ac.za]
Sent: 18 April 2007 14:38
To: keith.morris-at-ucl.ac.uk

This Question was submitted to Ask-A-Microscopist by
(akoorts-at-medic.up.ac.za)
from
http://www.msa.microscopy.org/Ask-A-Microscopist/Ask-A-Microscopist.html on
Wednesday, April 18, 2007 at 06:36:15
Remember to consider the Grade/Age of the student when considering the
Question
---------------------------------------------------------------------------
Please reply to both akoorts-at-medic.up.ac.za as well as to the Microscopy
Listserver
---------------------------------------------------------------------------

Email: akoorts-at-medic.up.ac.za
Name: Alida Koorts

Organization: University of Pretoria

Education: Graduate College

Location: Pretoria, South Africa

Question: Are there any software available to count gold particles
(immunolocalization) on TEM photo's?

---------------------------------------------------------------------------

==============================Original Headers==============================
7, 11 -- From zaluzec-at-ultra5.microscopy.com Wed Apr 18 08:33:50 2007
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7, 11 -- To: microscopy-at-microscopy.com
7, 11 -- From: akoorts-at-medic.up.ac.za (by way of Ask-A-Microscopist)
7, 11 -- Subject: AskAMicroscopist: count gold particles
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==============================Original Headers==============================
35, 24 -- From keith.morris-at-ucl.ac.uk Sat Apr 21 09:12:21 2007
35, 24 -- Received: from smtp1.global.net.uk (smtp1.global.net.uk [80.189.94.53])
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35, 24 -- From: "Keith Morris" {keith.morris-at-ucl.ac.uk}
35, 24 -- To: {akoorts-at-medic.up.ac.za}
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From: gary-at-gaugler.com
Date: Sat, 21 Apr 2007 15:15:17 -0500
Subject: [Microscopy] Re: New SEM Purchase

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

You are the one to say what you do or don't want. Unless
you mean specific brands and/or models of systems.

Buying a new SEM can be a joy and a headache. I can't imagine
anything worse than buyer's remorse when what you bought
is not what you really needed. To be sure, have a demo for
each system you are considering. Bring some typical specimens
you need imaged. Also look under the hood (inside the plinth,
cabinets, etc.). This will give you an idea of the level
of construction technology the tool is based on. You can
also find out how well or badly the SE detector works at
low vacuum. At up to about 8KX, they tend to work OK.

For low vacuum work, an ESEM is probably what you need. Another
option is the Zeiss EVO 50 with LaB6 (rather than W). It has
the XY movement you want but not as much Z, but it should be plenty.
As far as support is concerned, Zeiss has said that they will
support instruments for ten years after end of production.
Other companies have their own policy. Find out what it is.
The Amray SEMs are easy to fix and in my experience, were quite
reliable. The new SEMs are quantum leaps in column technology
and electronics, not to mention the extent of computer control.

Modern SEMs are digital capture. This is excellent. Native TIFF is
perfect for image processing. Analog (film) output is a
hassle since one must scan it to digital anyway to use the image.
Most current SEMs do not even include Polaroid/Graphloc backs.
At a minimum, the captured image will need brightness and contrast
adjustment. Some systems produce indexed color TIFF and these
require stripping the color off to make the picture look good.
This is easy to do with a Photoshop action. Once converted,
additional processing can be applied to enhance the area of
interest or add contrast to different layers. This may not
be necessary for biological specimens but it is quite useful
for metallurgical and semiconductor specimens. In this
respect, there is no issue of "honesty." The purpose of the
picture is to reveal structure, do failure analysis, evaluate
fabrication processing, etc.

Another factor that gets little attention is the design of
the column and final lens. For an environmental SEM, this
likely does not apply. But the issue is whether the final
lens is magnetic immersion or electrostatic. With a
magnetic immersion system, it does not like Ferrous specimens.
The electrostatic system does not care.

As for EDS, much has changed in the last year. Cryo cooled Si(Li)
detectors have problems and are likely to go away. With the advent
of new generation Peltier cooled Silicon Drift Detectors (SDD),
I suspect that LN2 dewar Si(Li) detector's days are numbered.

The past problem (among others) with SDDs was the change/decrease
in resolution as counts increased. Si(Li) does not do this.
The current generation of SDDs with the FET integrated onto the
detector chip have pretty much eliminated this problem. In addition
to the ability to handle very high counts, the SDDs are quiet, small
and almost instant-on. Do the research to find the SDD that has
optimum characteristics. If LN2 is not a bother for you, then
going with a Si(Li) dewar detector is probably significantly
cheaper than a new generation SDD. Either way, get a EDS "system."
One brand of detector and software.

You should prepare a statement of requirements that lists ALL of
the features and limits you need. Take your specimens and the
requirements list to demo sites. You will then get a good feel
for current generation SEMs and EDS. Then, modify your requirements
accordingly. If several company's products work for you, then
it is just the bid process to select your system.

Let us know how it goes. Since you have one shot at the well,
drink deeply. Hopefully you will not wind up saying "If only
I'd ....."

gary g.



At 09:50 AM 4/20/2007, you wrote:
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From: drteddunne-at-yahoo.com
Date: Sun, 22 Apr 2007 03:49:14 -0500
Subject: [Microscopy] Re: Recommended humidity level

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

My opinion is that less than 40% humidity is ideal.

Ted Dunn
The EMscope Company Ltd.
Thailand


--- TJJ-at-stowers-institute.org wrote:

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} Can anybody give me an optimal % relative humidity
} that is recommended
} for EM rooms? We recently had some failures with
} formvar grids (we
} think) due to excessive room humidity when they were
} being made. I can
} bring in a de-humidifier, but what would be
} considered to be optimal?
}
} Teri Johnson, HT(ASCP)QIHC
} Managing Director Histology Facility
} Stowers Institute for Medical Research
} 1000 E. 50th St.
} Kansas City, MO 64110
}
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From: r.sims-at-auckland.ac.nz
Date: Sun, 22 Apr 2007 18:12:18 -0500
Subject: [Microscopy] 840 water flows

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi Justin

You'll be lucky to find a coolant less viscous than water, particularly
one with such low cost and toxicity!

For what its worth, with 5 bar (about 75psi) supply pressure, I get

2.0 litres/min thru the diff pumps
1.0 l/min thru the electronics
0.15 l/min thru the OL
ie total around 3.2 l/min.

these are lower flows than the JEOL recommendations of 3.0, 1.5, and 0.5
ie total 5.0 l/min, but the combined discharge water is only 4 deg C
warmer than the supply and none of the lines feels particularly warm,
so all seems well. My 840 hasn't been flushed out for years, its on my
to-do-when-I-have-time list.

Your Iwaki pump probably lacks sufficient grunt for this application, 2.1
metres water head is only about 3psi, which has no chance of shifting
enough water through the 840.

Don't attempt to run the scope until you sort this out (buy a bigger
pump), the DPs have overtemp switches, and the electronics is
protected provided you set the little switch on the fuse panel to 'AUTO',
but there is no thermal protection for the OL, and you certainly don't
want to burn that one out.

good luck with the project

cheers

rtch

On 20 Apr 2007 at 17:44, kraftpiano-at-gmail.com wrote:

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} Sorry, I wasn't very clear about the chiller before. It's not a name
} brand chiller- it's actually a part from a larger system, but I don't
} know what that larger system is- I bought it locally as industrial
} surplus. Here's what I know about the recirculator system:
}
} Pump: Iwaki Magnetic drive pump. 12 L/min. Max. head 2.1m.
}
} There is a heat exchanger unit and all of the condenser piping
} necessary to chill the water, and it can divide the output a maximum
} of three ways, so I can have the electronics set on a different water
} circuit than the diffusion pumps. When I say that the pressure is not
} enough to push the water through, I mean that the pump pumps, but very
} little water is pushed through, and it is shutting down because of
} thermal overload. I know that the JEOL manual specifies 5 L/min. at
} 12-36 PSI, but I'm not sure how that translates from "Max head" to
} PSI. The pump's flow rate is more than enough to handle it, but it
} isn't making it through. That's why I was thinking about lower
} viscosity fluids, which should flush through at a higher flow rate and
} a lower PSI.
}

--
Ritchie Sims Ph D Phone : 64 9 3737599 ext 87713
Microanalyst Fax : 64 9 3737435
Department of Geology email : r.sims-at-auckland.ac.nz
The University of Auckland
Private Bag 92019
Auckland
New Zealand


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From: beaurega-at-westol.com
Date: Mon, 23 Apr 2007 07:51:02 -0500
Subject: [Microscopy] Re: SEM: Replacing diffusion pump water cycle

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi

I have probably purchased more electron microscopes than anyone else in the
world having acted as a consultant on an average of two or three purchases a
year over the past 25 years!

The summary of what I have learned is not to eliminate a microscope until
you have seen it in action on your specimens! My other point is not to
close your mind on future applications. An aircraft engine company were
pushed by me into purchasing a FEG instrument. In the first week they found
that their ideas of not going above 20,000X and below 15kV were blown away,
the additional information they could see was "mind blowing" and critical.

A third area of my concern is the selection of specimens and the clients
attitude during a demonstration. As an exdemonstrator for Hitachi, JEOL and
ISI I found that many prospective customers fight a silly battle with the
demonstrator. Firstly, one often found that quite often the client had not
looked at the specimens they had brought they were from another person in
the lab! In other cases the game is for the demonstrator, with no help from
the client, is expected to produce more and better information in one day
than the client has produced over many years. The problems deepen because
the client does not try to inform the demonstrator and help the
demonstration to bring out the critical data. After all it should not be a
test of the demonstrator but better a test of the microscope, most people
are buying the best microscope not the best demonstrator but that is
difficult to see in some demonstrations ;)

Time and time again the eventual purchase is not the instrument that we
start off believing is the best for the client. I have written
presentations on instrument purchase all too long to fit in here but
available on our web site in hints and tips or in a past edition of
Microscopy Today.

I hope this helps?

Steve Chapman
Protrain for EM training & consultancy world wide
www.emcourses.com
Tel +44 1280 816512 Fax +44 1280 814007
Mobile +44 7711 606967


----- Original Message -----
X-from: {gerard.cox-at-goodrich.com}
To: {protrain-at-emcourses.com}
Sent: Friday, April 20, 2007 6:48 PM

Hi,

According to Bernoulli:
Static PSI = height* specific gravity/ 2.31
2.31 feet of water is 1 PSI

Your PSI = 6.8 ft * 1 /2.31 = 2.9 PSI of STATIC HEAD

I had a system in a fan loft three stories higher than the lab. The back
pressure was about 15 PSI. So 3 stories is about 34 feet of static head.
So 34 feet is to ~15 PSI as 6.8 feet is to X

X = ~3.0 PSI for 2.1 meters of STATIC HEAD.

If the fluid is moving, the pressure will be less.

Loss of Head = V²/(2 * 32.2 feet / sec²)
At 1 foot per second,
Loss of Head = 1/(2*32.2) = 0.016 PSI or almost zero.

You need more pressure from a different direct drive pump, IMHO.

Flow rate: Your quoted flow rate might be and appears to me to be at no
head pressure. Flow will decrease as the head pressure is increased from
back pressure.

Thermal load? Most DP use at least 600 watts and usually more with
Santovac. So your system must have a cooling capacity of at least 600
watts and you probably need to dump 1500 watts of heat as a minimum due to
losses from cooling lines.

FYI Notes:
The green color in restricted cooling lines is usually the green compound
copper carbonate, (CuCO3) or basic copper carbonate. Other materials and
compounds are involved. The scale can be removed with minimal damage to
lens tubing, if that's the problem but I don't think that is it in this case.

Maintaining a balance of the chemistry in a chiller requires an
understanding of the Langalier index to make or remove scale in-situ. The
copper carbonate Ksp value I calculated years ago on paper was eliminated
by zealots of records retention. I just recalculated it. The solubility
used was 0.28 mg per 100 mls, an average value I found on the Internet for
copper carbonate.
Ksp CuCO3 = 4.96 * 10^(-14)
Ksp CaCO3 = 4.8 x 10^(-9) (Skoog and West)
or [0.87 x 10^(-8) in the CRC Handbook]
So GREEN copper carbonate will PPT before CaCO3 but it is similar to CaCO3
in that both have limited solubility. The amount of calcium from
contamination by dead volumes involved in using city water and improper
dead volume flushing, should not increase like copper ions do. The green
color and the Ksp value of copper carbonate can be used as a "colorimetric
spot test". I used this test. All plastic pipes will not save you from
copper. Fittings and pump heads are made of brass.

CaCO3, CuO and carbonates of copper are involved as well as the pH and CO2
gas mixing. The scaling can be tracked by observing the color of
semitransparent PP tubing in an Edwards 306A or an equivalent transparent
tubing somewhere in your system. If you see a green color forming as a
lining in the tubing, then the Ksp [ion concentration product] has been
exceeded. You need to remove some copper ions and replace that water with
distilled water. Don't remove all the "old" water. Leave some ions behind
to mix with the new DI water. This is easy to do in a properly designed
system with a chilled water line that can divert contaminated water into a
lab sink and that also has an automatic DI water refill on the chiller
reservoir.

Disclaimers and simple water tests:
Copper ions kill algae.
Quaternary ammonium salt surfactants (used in swimming pools) kill algae by
breaking open cell walls.
Adding ammonium hydroxide to a sample of chiller water containing copper
ions causes a deep blue color to form at high pH.
Chloride ions cause stainless steel to pit corrode.
Most DPs and some tubing fittings are made of SS.
Silver nitrate solution forms a white precipitate when added to a chilled
water sample with chloride ions in it.
Any form of available chlorine like chloramine-T or isocyanurates will be
reduced to chloride ions over time. Do you really want cyanuric acid or
p-toluene-sulfonamide in your system?
Using all plastic pipes and an HVAC heat exchanger system to supply
chilling, will not save you from copper ions forming.

Paul


At 05:43 PM 4/20/07 -0500, you wrote:
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From: cammer-at-aecom.yu.edu
Date: Mon, 23 Apr 2007 08:41:26 -0500
Subject: [Microscopy] IPLab with ASI stage does not work, ask for help and potential

Contents Retrieved from Microscopy Listserver Archives
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Our ASI stage with MS-2000 controller has not worked properly with
IPLab for years. Back with IPLab versions 3.65 and earlier we wrote
our own scripts to get around the problem, but with the upgrade to
4.0.# the ASI stage completely does not work with the IPLab software.

For *more*than*a*year* we have been asking Scanalytics / BD
BioSciences to fix this problem and even though we have had visits on
site, the problem is not solved. We invested in multiple license
upgrades, and two of the systems simply don't work.

Does anybody know how to operate the ASI stage with a PC running IPLab 4.0.#?

At this point we are desperate to have our two inverted microscopes
with mechanical stages work properly and unless this email to a
public listserv acts as a motivator, I am ready to give up on IPLab
as a software solution for our light microscopy needs and BD
Biosciences as truly responsive to customers.

-Michael Cammer
____________________________________________________________________________
Michael Cammer Analytical Imaging Facility Albert Einstein Coll. of Med.
URL: http://www.aecom.yu.edu/aif/


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From: TJJ-at-stowers-institute.org
Date: Mon, 23 Apr 2007 09:56:05 -0500
Subject: [Microscopy] FW: Recommended humidity level

Contents Retrieved from Microscopy Listserver Archives
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Thanks for all your replies. Just to clarify, this will be in a sample
prep area only, the scope is in a different room. The ventilation in
this room is "weird" (the best way I can describe it), most of the time
it's not an issue. On occasion though, you can walk in to the room from
the hallway and the atmospheric conditions are totally different.

I'm thinking between 30 and 40% sounds about right.


==============================Original Headers==============================
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From: tivol-at-caltech.edu
Date: Mon, 23 Apr 2007 11:35:09 -0500
Subject: [Microscopy] 2nd for posting to the list

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On Apr 20, 2007, at 6:49 PM, gary-at-gaugler.com wrote:

} The reason NOT to post to the list is that you get
} volumes of "Out Of Office" messages. This is the
} same as when you make a new posting. Most of the
} defunct messages are trapped by Eudora but quite
} a few still get though....sigh.
}
} Some do not have this subject but say that they
} are gone from xx to yy.
}
Dear Gary,
Is it possible to have all OOO messages have the subject line be "Out
Of Office"? If so, Nestor could request it, but if the company that
one works for has a standard OOO heading, that may be impractical.
Yours,
Bill Tivol, PhD
EM Scientist
Electron Cryo-Microscopy Facility
Broad Center, Mail Code 114-96
California Institute of Technology
Pasadena CA 91125
(626) 395-8833
tivol-at-caltech.edu


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From: jrunions-at-brookes.ac.uk
Date: Mon, 23 Apr 2007 11:38:24 -0500
Subject: [Microscopy] Masters course in Bioimaging - Oxford Brookes

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Dear Microscopists,

We are pleased to announce that the Oxford Brookes University Masters
course in Bioimaging will begin in Sept. 2007. There is still room for
students and information about the course can be found at the following
link:

https://www.brookes.ac.uk/studying/courses/postgraduate/2007/bmt

We will run this as a modular one year full time course intended to
teach microscopy (light / confocal / em) and associated laboratory skills.

If you know of students or professionals that might be interested,
please can you pass this information to them. Please contact me if you
need more detailed information or if you would like a pdf that provides
details of the course.

Sincerely, John.
--

*********************************
C. John Runions, Ph.D.
School of Life Sciences
Oxford Brookes University
Oxford, UK
OX3 0BP

email: jrunions-at-brookes.ac.uk {mailto:jrunions-at-brookes.ac.uk}
phone: +44 (0) 1865 483 964

web: http://www.brookes.ac.uk/lifesci/runions/HTMLpages/index.html




New - Oxford Brookes Master's in Bioimaging with Molecular Technology
{https://www.brookes.ac.uk/studying/courses/postgraduate/2007/bmt}


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From: monroe-at-emcenter.msstate.edu
Date: Mon, 23 Apr 2007 15:02:18 -0500
Subject: [Microscopy] MSA 2007 Meeting: Request for Student Volunteers (Bursaries)

Contents Retrieved from Microscopy Listserver Archives
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Greetings,

This is the first announcement for students who will attend the
Microscopy and Microanalysis Meeting in Ft. Lauderdale, Fl, August
5-9, 2007 and would like to apply for a Student Bursary to help
defray meeting costs. The complete description of the Bursary is
listed below, including the registration process.

The contact persons this year who will coordinate the student volunteers are;

Bill Monroe monroe-at-emcenter.msstate.edu
Amanda Lawrence lawrence-at-emcenter.msstate.edu
Mike Miller millem1-at-auburn.edu


STUDENT BURSARIES

The Microscopy Society of America values student members and
recognizes that they are the future of both the society and the field
of microscopy in general. MSA is therefore pleased to offer student
bur-saries of $200 to registered students. The most important purpose
of these bursaries is to encourage students to attend the annual
MSA/MAS Microscopy and Microanalysis meeting, where these young
sci-entists can meet and interact with the established microscopy
community as well as assisting with the meeting.

Each bursary recipient will be expected to work for a minimum of 20
hours during the meeting and/or at the pre-meeting weekend events. A
student may work up to an additional 20 hours, for a total of 40
hours. These extra hours will add to the bursary total at a rate of
$10 per hour. The maximum bursary will therefore be $400. The duties
will involve, but are not necessarily limited to, providing support
in symposia (helping with audio-visual needs, maintaining an
attendance count, and helping speakers set up for their
presentation), staffing the MSA Megabooth, and monitoring use of the
Internet Cafe. Applicants for the bursaries must be members of MSA or
MAS, and enrolled as students at a recognized educational
institution. All MSA or MAS student members are eligible for
bursaries, including those who are recipients of MSA Presidential
Scholars Awards and MAS Distinguished Scholar Awards. Eligible
students may apply for bursaries when registering for the conference
on the conference website, or at on-site registration. Bursaries are
limited and early application is encouraged.
How it works:

The registration form for the meeting will have a check box
indicating that the applicant is a registered student and is
requesting a bursary. The check box will have a note beside it
reminding the applicant that the bursary requires them to work at the
meeting. Students who have applied for bursaries will receive letters
from MSA explaining the conditions that they need to satisfy in order
to receive the bursaries. The tasks at the meeting will be allocated
by the Student Worker Organizers Sub-Committee of the Education
Committee. When students pick up their registration materials at the
meeting, they will receive assignment forms indicating the specific
tasks they are to perform, and the person(s) they need to contact in
order to carry out those tasks. Each stu-dent's assignment forms must
be signed by all of the contact persons listed, indicating that all
assigned tasks have been performed. Upon completion of assignments
and submission of the signed forms, the bursary check will be issued
by the appropriate representative at the registration desk.


Should you have questions concerning the process, please contact:

Bill Monroe monroe-at-emcenter.msstate.edu




--
Bill Monroe
Electron Microscope Center
103 Clay Lyle Entomology Building
Mississippi State University
Mississippi State, MS 39762
(662)-325-3019 Work
(662)-323-5246 Home
(662)-325-0246 Fax

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From: amich-at-ufl.edu
Date: Mon, 23 Apr 2007 15:57:57 -0500
Subject: [Microscopy] cationic dyes for SEM bacterial visualization

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html


Dear Servers,

Recently I started working on visualization of bacteria on various
biocidal surfaces. I have been soliciting advices regarding
samples prep with excellent success for which I should thank
Servers.
I have new question regarding implementation of cationic dyes for
SEM bacterial visualization. Considering that I am primarily
looking for changes (sometimes very subtle) in bacterial
appearance due to the biocide action I am concern that some of the
changes could be introduced by fixation/processing artifacts. Will
addition of cationic dye to glutaraldehyde/osmium tetroxide
protocol help me to preserve fine structures? Which dye would be
best and in which concentration? Would it make difference for
gram-positive as much as gram ?negative strains?
Thank you in advance,
Albina

--
MIKHAYLOVA,ALBINA, PhD
Materials Science and Engineering
University of Florida
PO Box 116400
Gainesville, Florida 32611
Phone: (352) 392-6533
Fax: (352) 392-3771
E-Mail: amich-at-ufl.edu


==============================Original Headers==============================
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5, 22 -- From: "MIKHAYLOVA,ALBINA" {amich-at-ufl.edu}
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From: gwe-at-ufl.edu
Date: Mon, 23 Apr 2007 16:50:15 -0500
Subject: [Microscopy] Re: cationic dyes for SEM bacterial visualization

Contents Retrieved from Microscopy Listserver Archives
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Both ruthenium red and alcian blue can be used. In addition cetyl
pyridimium chloride is also a choice for preserving negatively charged
mucopolysaccharides that are on the surface of some cells. The tendency
is to overly decorate these surface coats and obscure real detail.
These reagents do nothing to preserve the actual cell or the cells wall.
I also think that SEM is not the tool for seeing any subtle effects.
Work I had done some years ago required thin section TEM and even then
only catastrophic changes were evident i.e. lysis or cytoplasmic
partitioning. Changes in membrane architecture might require freeze
fracture EM.
To minimize fixation artefacts for SEM you might try rapid freezing
followed by freeze drying; freeze substitution fixation followed by
critical point drying or cryo-SEM of fully hydrated cells. In all three
of these techniques very rapid freezing is required in order to prevent
ice crystal formation that would cause artefact in and of itself.
There is a book in the UF library by Aldrich and Taylor that discusses
in more detail some of the things that I have mentioned. I think the
title is "Ultrastructure Techniques for Microorganisms". It is old, but
many of the techniques are still in use today. I believe that I left my
personal copy at the ICBR EM Core Lab, when I retired.

amich-at-ufl.edu wrote:
} ----------------------------------------------------------------------------
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} ----------------------------------------------------------------------------
}
}
} Dear Servers,
}
} Recently I started working on visualization of bacteria on various
} biocidal surfaces. I have been soliciting advices regarding
} samples prep with excellent success for which I should thank
} Servers.
} I have new question regarding implementation of cationic dyes for
} SEM bacterial visualization. Considering that I am primarily
} looking for changes (sometimes very subtle) in bacterial
} appearance due to the biocide action I am concern that some of the
} changes could be introduced by fixation/processing artifacts. Will
} addition of cationic dye to glutaraldehyde/osmium tetroxide
} protocol help me to preserve fine structures? Which dye would be
} best and in which concentration? Would it make difference for
} gram-positive as much as gram ?negative strains?
} Thank you in advance,
} Albina
}
} --
} MIKHAYLOVA,ALBINA, PhD
} Materials Science and Engineering
} University of Florida
} PO Box 116400
} Gainesville, Florida 32611
} Phone: (352) 392-6533
} Fax: (352) 392-3771
} E-Mail: amich-at-ufl.edu
}
}
} ==============================Original Headers==============================
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}

--
Greg Erdos
University of Florida, Retired
Micanopy, Florida

==============================Original Headers==============================
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From: mtlrgist-at-aol.com
Date: Mon, 23 Apr 2007 18:08:54 -0500
Subject: [Microscopy] viaWWW: Zeiss DSM 950 External Scan Interface

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This Question/Comment was submitted to the Microscopy Listserver
using the WWW based Form at http://microscopy.com/MicroscopyListserver/MLFormMail.html
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Email: mtlrgist-at-aol.com
Name: Michael Neff

Organization: MNA, CofC

Title-Subject: [Filtered] Zeiss DSM 950 External Scan Interface

Question: I would like to obtain and install an external scan interface for my Zeiss DSM-950. I believe that any ESI from the DSM series scopes will work. Does anybody know of a retired machine with this card in it? Is anybody out there knowledgeable in installing said interface.

---------------------------------------------------------------------------

==============================Original Headers==============================
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From: A.A.Evans-at-Bradford.ac.uk
Date: Tue, 24 Apr 2007 08:01:00 -0500
Subject: [Microscopy] LSCM data and anaglyphs

Contents Retrieved from Microscopy Listserver Archives
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Hi All,

Can anybody direct me to software for producing anaglyphs from 3d data I
have acquired using my LSCM? Preferably software which is free or available
as a trial.

thanks

-----------------------
Adrian A. Evans



==============================Original Headers==============================
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From: phillipst-at-missouri.edu
Date: Tue, 24 Apr 2007 09:13:08 -0500
Subject: [Microscopy] spinning disks

Contents Retrieved from Microscopy Listserver Archives
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Our imaging facility is considering acquiring a spinning disk confocal to
compliment our 2 laser scanning instruments (Radiance 2000, Zeiss 510 NLO
META). The leading configurations are the Yokogawa and Olympus DSU units
with an EMCCD. I would appreciate insight on the following issues: Are
service contracts on the spinning disk unit or EMCCD essential (I have them
on my LSMs)? For those of you running core facilities, does the spinning
disk siphon a significant proportion of users off the LSMs or do you find
its use restricted to live cell/fast acquisition studies? And finally, how
much does going with laser excitation really improve things over the use of
a mercury arc or metal halide illumination source? Thanks for any comments
you have on this. Tom



Thomas E. Phillips, PhD
Professor of Biological Sciences
Director, Molecular Cytology Core
2 Tucker Hall
University of Missouri
Columbia, MO 65211-7400

573-882-4712 (office)
573-882-0123 (fax)
PhillipsT-at-missouri.edu
http://www.biology.missouri.edu/faculty/phillips.html
http://www.biotech.missouri.edu/mcc/


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From: drteddunne-at-yahoo.com
Date: Tue, 24 Apr 2007 10:47:26 -0500
Subject: [Microscopy] Re: FW: Recommended humidity level

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Don't drop the humidity too low or static charge
becomes at least annoying and at worst a problem.

I would say 35% at the lowest.


Ted Dunn
The EMscope Company Ltd.
Thailand
--- TJJ-at-stowers-institute.org wrote:

} ----------------------
}
} Thanks for all your replies. Just to clarify, this
} will be in a sample
} prep area only, the scope is in a different room.
} The ventilation in
} this room is "weird" (the best way I can describe
} it), most of the time
} it's not an issue. On occasion though, you can walk
} in to the room from
} the hallway and the atmospheric conditions are
} totally different.
}
} I'm thinking between 30 and 40% sounds about right.
}
}
} ==============================Original
} Headers==============================
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__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
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From: beaurega-at-westol.com
Date: Tue, 24 Apr 2007 22:11:56 -0500
Subject: [Microscopy] Request for 1964 Norelco Reporter Article or Page

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi,

I would like to know if anyone has an old 1964 copy of a Norelco Reporter.
I am interested in an article, opinion, or the writings by:

"R. E. Ogilvie, Norelco Reporter, 11, 75 (1964)".
(The reference gave no title but it might contain the words electron gun or
filament.)

I could not locate this magazine or booklet at any library on WorldCat.Org.

If you scan or send it, please notify list members so that we don't
duplicate efforts.

Thank you in advance for any help you can provide.

Paul Beauregard
144 Chapel View Drive
Greensburg, PA 15601
724-834-2247

==============================Original Headers==============================
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From: michael-at-shaffer.net
Date: Wed, 25 Apr 2007 08:10:15 -0500
Subject: [Microscopy] SEM standards for imaging

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hello MSA'rs :o)

I need an imaging standard that would allow me to check the magnification
and distortions present for our SEM. A good example is the set of SIRA
gratings, but I thought I'd put it to the list for finding the most
versatile reference standard relative to cost. My needs are (1) to check
magnification in x & y for high and low mag, (2) to check orthogonality at
high and low mag, and (3) to check for barrel, pin-cushioning, or
trapazoidal distortions, at high and low mag ... Where high and low mag are
} 2000x and {500x.

Tia & cheerios from "the rock" :o)
michael shaffer

SEM/MLA Research Coordinator
{http://www.mun.ca/creait/maf/}
Inco Innovation Centre
Memorial University
St. John's, Newfoundland



==============================Original Headers==============================
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5, 18 -- From: "michael shaffer" {michael-at-shaffer.net}
5, 18 -- To: "MSA Microscopy list" {Microscopy-at-microscopy.com}
5, 18 -- Subject: SEM standards for imaging
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From: NWWhite-at-bwxt.com
Date: Wed, 25 Apr 2007 08:32:50 -0500
Subject: [Microscopy] SEM standards for imaging

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hello Michael,

I am using the Geller
(http://www.gellermicro.com/mag_standards/mrs.html) MRS-3. It sure is
not inexpensive, but should do what you want. ...There are newer
versions as well. Be advised the standards are traceable to NPL rather
than directly to NIST. Joe Geller should have a web link available
indicating an agreement between NIST and NPL (UK) to accept each others
certifications. This satisfied my QA department. No connection with
Geller other than a satisfied customer.

Woody White
BWXT Services



-----Original Message-----
X-from: michael-at-shaffer.net [mailto:michael-at-shaffer.net]
Sent: Wednesday, April 25, 2007 9:11 AM
To: White, Woody N.

Hello MSA'rs :o)

I need an imaging standard that would allow me to check the
magnification
and distortions present for our SEM. A good example is the set of SIRA
gratings, but I thought I'd put it to the list for finding the most
versatile reference standard relative to cost. My needs are (1) to
check
magnification in x & y for high and low mag, (2) to check orthogonality
at
high and low mag, and (3) to check for barrel, pin-cushioning, or
trapazoidal distortions, at high and low mag ... Where high and low mag
are
} 2000x and {500x.

Tia & cheerios from "the rock" :o)
michael shaffer

SEM/MLA Research Coordinator
{http://www.mun.ca/creait/maf/}
Inco Innovation Centre
Memorial University
St. John's, Newfoundland



==============================Original
Headers==============================
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From: zaluzec-at-microscopy.com
Date: Wed, 25 Apr 2007 08:38:23 -0500
Subject: [Microscopy] SEM Magnification Standard

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Michael

There is a NIST & ISO-17025 traceable Magnification standard available from
Geller Microanalytical Lab.

http://www.gellermicro.com/mag_standards/mrs.html

It has applications to many microscopies including SEM.

Disclaimer: I have no financial interests in the product.


Nestor
Your Friendly Neighborhood SysOp

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From: edelmare-at-muohio.edu
Date: Wed, 25 Apr 2007 15:42:26 -0500
Subject: [Microscopy] Question of Terminology - "Microprobe"

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

O.k., folks Lets see if the Microscopy and Microanalysis community
can come an agreement.

Traditionally the term "Microprobe" has been used to refer to a
dedicated wave length dispersive x-ray microanalysis
microscope/instrument (XWDS or WDS). Is this still a valid use for
the the term "Microprobe"? Or is it antiquated?

. . . because it comes into conflict a "newer" use of the word
"microprobe" as refering to a "small" physical probing device,
typically mechanical, for manipulating or testing small items. Would
these probing-manipuating-testing devices be better called
"Nanoprobes" (even thought they may actually handle items / objects
in the micrometer to 100's-micrometer range).

Context will NOT sufice to distinguish between the two as
microscopists now deal with both.

Anyone care to share comments or opinions ?


Richard E. Edelmann, Ph.D.
EXPO Editor, Microscopy and Microanalysis Supplement
Electron Microscopy Facility Director
364 Pearson Hall
Miami University, Oxford, OH 45056
Ph: 513.529.5712 Fax: 513.529.4243
E-mail: edelmare-at-muohio.edu
http://www.emf.muohio.edu


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From: tom-at-farrarlaw.net
Date: Wed, 25 Apr 2007 18:26:52 -0500
Subject: [Microscopy] viaWWW: Water Beading

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

I still associate microprobe with the scanning electron beam device
equipped with wavelength spectrometers for the express purpose of x-ray
microanalysis.

I refer to the little thing used to hold and move objects around as
micro-manipulators.

I will admit that micro-probe can refer to a lot of things. I wouldn't
be surprised if the microelectronics folks adopted the term to refer to
a microscopic test lead. I also suppose the scanning probe microscope
folks could refer to their tips as microprobes. But to me, a microprobe
will be those things like ARL used to make.

Maybe that makes me old school, but it seems like a decent working
definition. I am getting old enough people probably expect me to be a
bit pig-headed and crotchety anyway. I might as well live up to it. {g}

Warren Straszheim


-----Original Message-----
X-from: edelmare-at-muohio.edu [mailto:edelmare-at-muohio.edu]
Sent: Wednesday, April 25, 2007 3:44 PM
To: wesaia-at-iastate.edu

This Question/Comment was submitted to the Microscopy Listserver
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Email: tom-at-farrarlaw.net
Name: R. Thomas Farrar

Title-Subject: [Filtered] Water Beading

Question: Within the past year or so I read that scientists had discovered the reason why water beads on lily pads. Recently I have had need for the article (more accurately, for the reason why the water beading occurs) and have searched for it without success. Google led me to this forum, and I wonder whether anyone can help this non-scientist to the people who made the discovery?

---------------------------------------------------------------------------

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From: forbes-at-essential-research.com
Date: Wed, 25 Apr 2007 18:27:27 -0500
Subject: [Microscopy] viaWWW: ISI Sputter Coater

Contents Retrieved from Microscopy Listserver Archives
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Email: forbes-at-essential-research.com
Name: David Forbes

Organization: Essential Research

Title-Subject: [Filtered] ISI Sputter Coater

Question: I'm trying to resurrect an old ISI Sputer Coater Model POL4172 - without a manual. All the components are present, but the operation seems to be questionable. Particularly scary is that when the unit is plugged in, the high voltage is on and plasma strikes right away. It seems that this should wait until I dial on the HV. Any suggestions on troubleshooting or getting a manual would be helpful.
I suspect this type of unit is primarily for Au sputtering, but some ideas have been floating around about sputtering more exotic materials (oxides). Any place I can find guidance about sputtering conditions for different materials?

Thanks!


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From: frah0010-at-umn.edu
Date: Wed, 25 Apr 2007 18:30:27 -0500
Subject: [Microscopy] Re: Question of Terminology - "Microprobe"

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi all,

I'd argue that "microprobe" isn't a complete term for anything.

The word "microprobe" can describe dozens of different instruments or
devices.

Off the top of my head:

- Electron Microprobe (as in the JEOL type)
- Laser Ablation "Microprobe" ICP-MS
- Ion "Microprobe" Mass Spectrometer (SIMS)
- NASA's new small space probes are called microprobes
- Anything with a small sensor or feedback device or manipulator

Consequently, if one is referring to the SEM-like device with WDS,
one must call it an electron microprobe, not just a microprobe
(except in informal settings where the context is known).

If one is talking about SIMS, one must talk about an ion microprobe.
If one is discussing the Deep Space 2 mission, one should call it a
space microprobe or something like that. I'd like Warren's term of
"micro-manipulators," but one could call them manipulator microprobes
or something similar.

Calling the manipulating devices in question "nanoprobes" is not
better because that, too, could describe a lot of different devices
-- there are already small optical devices called nanoprobes, and the
field of "nanoprobes" will only get more crowded in coming years.

Also some, no doubt, will assert that "electron microprobe" isn't the
formal term anyway and that the instrument is more properly called an
"electron probe microanalyzer" instead. However, if S.J.B. Reed
calls it an electron microprobe, then so will I. If anything,
raising this point strengthens the above argument. One cannot just
call something a "microanalyzer" because that could be dozens or
hundreds of devices too. Instead, the full term is needed to
describe any instrument properly.

To summarize: "microprobe" really isn't a complete term that
describes anything specifically.

Cheers,
Ellery

--------------------
Ellery E. Frahm
Research Fellow & Manager
Electron Microprobe Laboratory
University of Minnesota - Twin Cities
Department of Geology & Geophysics
Alternate e-mail: elleryfrahm-at-mac.com
Lab Website: http://probelab.geo.umn.edu
Personal Website: http://umn.edu/~frah0010



On Apr 25, 2007, at 3:50 PM, edelmare-at-muohio.edu wrote:

} ----------------------------------------------------------------------
} ------
} The Microscopy ListServer -- CoSponsor: The Microscopy Society of
} America
} To Subscribe/Unsubscribe -- http://www.microscopy.com/
} MicroscopyListserver
} On-Line Help http://www.microscopy.com/MicroscopyListserver/FAQ.html
} ----------------------------------------------------------------------
} ------
}
} O.k., folks Lets see if the Microscopy and Microanalysis community
} can come an agreement.
}
} Traditionally the term "Microprobe" has been used to refer to a
} dedicated wave length dispersive x-ray microanalysis
} microscope/instrument (XWDS or WDS). Is this still a valid use for
} the the term "Microprobe"? Or is it antiquated?
}
} . . . because it comes into conflict a "newer" use of the word
} "microprobe" as refering to a "small" physical probing device,
} typically mechanical, for manipulating or testing small items. Would
} these probing-manipuating-testing devices be better called
} "Nanoprobes" (even thought they may actually handle items / objects
} in the micrometer to 100's-micrometer range).
}
} Context will NOT sufice to distinguish between the two as
} microscopists now deal with both.
}
} Anyone care to share comments or opinions ?
}
}
} Richard E. Edelmann, Ph.D.
} EXPO Editor, Microscopy and Microanalysis Supplement
} Electron Microscopy Facility Director
} 364 Pearson Hall
} Miami University, Oxford, OH 45056
} Ph: 513.529.5712 Fax: 513.529.4243
} E-mail: edelmare-at-muohio.edu
} http://www.emf.muohio.edu

==============================Original Headers==============================
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16, 20 -- Subject: Re: [Microscopy] Question of Terminology - "Microprobe"
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From: r.sims-at-auckland.ac.nz
Date: Wed, 25 Apr 2007 18:38:55 -0500
Subject: [Microscopy] Question of Terminology - "Microprobe"

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html


I'm releived that it's not just me who finds 'Electron Probe Micro Analyser' too much of a
mouthfull.

But we all use the acronym EPMA, rather than EMP, don't we?

cheers

rtch

On 25 Apr 2007 at 18:31, frah0010-at-umn.edu wrote:

}
}
}
} ----------------------------------------------------------------------
} ------ The Microscopy ListServer -- CoSponsor: The Microscopy Society
} of America To Subscribe/Unsubscribe --
} http://www.microscopy.com/MicroscopyListserver On-Line Help
} http://www.microscopy.com/MicroscopyListserver/FAQ.html
} ----------------------------------------------------------------------
} ------
}
} Hi all,
}
} I'd argue that "microprobe" isn't a complete term for anything.
}
} The word "microprobe" can describe dozens of different instruments or
} devices.
}
} Off the top of my head:
}
} - Electron Microprobe (as in the JEOL type)
} - Laser Ablation "Microprobe" ICP-MS
} - Ion "Microprobe" Mass Spectrometer (SIMS)
} - NASA's new small space probes are called microprobes
} - Anything with a small sensor or feedback device or manipulator
}
} Consequently, if one is referring to the SEM-like device with WDS,
} one must call it an electron microprobe, not just a microprobe
} (except in informal settings where the context is known).
}
} If one is talking about SIMS, one must talk about an ion microprobe.
} If one is discussing the Deep Space 2 mission, one should call it a
} space microprobe or something like that. I'd like Warren's term of
} "micro-manipulators," but one could call them manipulator microprobes
} or something similar.
}
} Calling the manipulating devices in question "nanoprobes" is not
} better because that, too, could describe a lot of different devices
} -- there are already small optical devices called nanoprobes, and the
} field of "nanoprobes" will only get more crowded in coming years.
}
} Also some, no doubt, will assert that "electron microprobe" isn't the
} formal term anyway and that the instrument is more properly called an
} "electron probe microanalyzer" instead. However, if S.J.B. Reed
} calls it an electron microprobe, then so will I. If anything,
} raising this point strengthens the above argument. One cannot just
} call something a "microanalyzer" because that could be dozens or
} hundreds of devices too. Instead, the full term is needed to
} describe any instrument properly.
}
} To summarize: "microprobe" really isn't a complete term that
} describes anything specifically.
}
} Cheers,
} Ellery
}
} --------------------
} Ellery E. Frahm
} Research Fellow & Manager
} Electron Microprobe Laboratory
} University of Minnesota - Twin Cities
} Department of Geology & Geophysics
} Alternate e-mail: elleryfrahm-at-mac.com
} Lab Website: http://probelab.geo.umn.edu
} Personal Website: http://umn.edu/~frah0010
}
}
}
} On Apr 25, 2007, at 3:50 PM, edelmare-at-muohio.edu wrote:
}
} } --------------------------------------------------------------------
} } -- ------ The Microscopy ListServer -- CoSponsor: The Microscopy
} } Society of America To Subscribe/Unsubscribe --
} } http://www.microscopy.com/ MicroscopyListserver On-Line Help


--
Ritchie Sims Ph D Phone : 64 9 3737599 ext 87713
Microanalyst Fax : 64 9 3737435
Department of Geology email : r.sims-at-auckland.ac.nz
The University of Auckland
Private Bag 92019
Auckland
New Zealand


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From: john.mardinly-at-intel.com
Date: Wed, 25 Apr 2007 20:36:49 -0500
Subject: [Microscopy] Question of Terminology - "Microprobe"

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hmmmmmmm-If my memory is correct, the Microprobe was invented by
Castaing around 1949. I don't know how he spelled it in French, but that
was what it was called, and there was little doubt that his Ph.D. thesis
describing the instrument and the theoretical physics behind it was
nothing less than extraordinary, so please give it the respect it will
always be due and don't try to rename it.

John Mardinly

Intel

This comment is not the opinion of Intel Corporation.

-----Original Message-----
X-from: edelmare-at-muohio.edu [mailto:edelmare-at-muohio.edu]
Sent: Wednesday, April 25, 2007 1:43 PM
To: Mardinly, John

O.k., folks Lets see if the Microscopy and Microanalysis community
can come an agreement.

Traditionally the term "Microprobe" has been used to refer to a
dedicated wave length dispersive x-ray microanalysis
microscope/instrument (XWDS or WDS). Is this still a valid use for
the the term "Microprobe"? Or is it antiquated?

. . . because it comes into conflict a "newer" use of the word
"microprobe" as refering to a "small" physical probing device,
typically mechanical, for manipulating or testing small items. Would
these probing-manipuating-testing devices be better called
"Nanoprobes" (even thought they may actually handle items / objects
in the micrometer to 100's-micrometer range).

Context will NOT sufice to distinguish between the two as
microscopists now deal with both.

Anyone care to share comments or opinions ?


Richard E. Edelmann, Ph.D.
EXPO Editor, Microscopy and Microanalysis Supplement
Electron Microscopy Facility Director
364 Pearson Hall
Miami University, Oxford, OH 45056
Ph: 513.529.5712 Fax: 513.529.4243
E-mail: edelmare-at-muohio.edu
http://www.emf.muohio.edu


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From: mganger-at-optonline.net
Date: Wed, 25 Apr 2007 20:49:16 -0500
Subject: [Microscopy] TEM help with fat biopsy

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Greetings all,

I have recently received fat pad aspiration biopsies where the fat that
was sent is very fine (no more than 20 cells together at it's largest,
most are smaller than that.)

If possible, I need a quick method whereby I can take this floating
material and condense it to a pellet for embedding in agarose. I do not
have the option of hand processing for TEM so transfering this material
into a intermediate media is a must.

Thanks in advance,

Mike Ganger


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From: beaurega-at-westol.com
Date: Wed, 25 Apr 2007 22:19:34 -0500
Subject: [Microscopy] Re: Request for 1964 Norelco Reporter Article or

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi,

My thanks to those that tried to help me find this obscure item from the
Norelco Reporter from 40 years ago. I was notified that the article was
located at a library and sent for.

This item was more like a newsletter or pamphlet from a company. That made
it hard to find, IMO. It appears that it did not end up with Philips
Electron Optics (FEI).

Libby, Phil, John, Tom, Ron, and Sharon; my special thanks to all of you.

Paul


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From: frah0010-at-umn.edu
Date: Wed, 25 Apr 2007 22:25:44 -0500
Subject: [Microscopy] Question of Terminology - "Microprobe"

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

On Apr 25, 2007, at 8:42 PM, john.mardinly-at-intel.com wrote:
}
} Hmmmmmmm-If my memory is correct, the Microprobe was invented by
} Castaing around 1949. I don't know how he spelled it in French, but
} that
} was what it was called, and there was little doubt that his Ph.D.
} thesis
} describing the instrument and the theoretical physics behind it was
} nothing less than extraordinary, so please give it the respect it will
} always be due and don't try to rename it.
}
} John Mardinly


Actually Castaing's 1951 thesis was titled "Application des Sondes
Electroniques a Une Methode d'Analyse Poncteculle Chimique et
Cristallographique" which roughly translates as "Application of
Electron Probes as a Method of Local Chemical and Crystallographic
Analysis." I'm not sure what he called his device in the thesis -- I
don't have a copy in French to check. Anyone?

I know that Castaing's 1953 paper with Guinier in "Analytical
Chemistry" calls it the "electronic microanalyzer." I believe,
though, when Cameca was developing their first commercial instrument,
they were using the word "microsonde" to describe it.

I'm not certain what Borovskii called his device in 1953. Nor do I
know what Hillier called the device he patented in 1947 -- the title
of his patent was something like "electron probe analysis employing x-
ray spectrography," I believe.

I don't think we should feel too obligated to use Castaing's
terminology (despite the problems presented by "microsonde" or
"electronic analyzer"). In science, we should be able to reclassify
things based on new definitions or better categories, such as
redefining planets to include extrasolar bodies but exclude Pluto and
other Kuiper Belt objects.

I do agree with John, though, because I don't want to order new
stationary.

Best,
Ellery

--------------------
Ellery E. Frahm
Research Fellow & Manager
Electron Microprobe Laboratory
University of Minnesota - Twin Cities
Department of Geology & Geophysics
Alternate e-mail: elleryfrahm-at-mac.com
Lab Website: http://probelab.geo.umn.edu
Personal Website: http://umn.edu/~frah0010


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From: oshel1pe-at-cmich.edu
Date: Thu, 26 Apr 2007 07:56:59 -0500
Subject: [Microscopy] RE: Question of Terminology - "Microprobe"

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html


Rtch writes ...

} I'm releived that it's not just me who finds 'Electron Probe
} Micro Analyser' too much of a mouthfull.
}
} But we all use the acronym EPMA, rather than EMP, don't we?

If that's a question and this is a poll, I'm in agreement. "EPMA" is the
defacto acronym, but there's no end to the number of us who still refer to
it also as a "microprobe".

Genuinely, Michael Shaffer :o)

SEM/MLA Research Coordinator
http://www.mun.ca/creait/maf/

Inco Innovation Centre
Memorial University
St. John's, Newfoundland



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From lucidic-at-virtual2.webair.com Thu Apr 26 05:28:32 2007
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I have to agree with Warren, especially perhaps his last paragraph.
"Microprobe" has a definite meaning to me and most microscopists.
I wouldn't suggest using "nanoprobe", as that doesn't really solve
the problem of confusing terms. Perhaps a simple addition of an
adjective to make it a noun phrase, like "mechanical microprobe".
Micromanipulator is a well-known term, so the next step would be
nanomanipulator. Let's start using that before some company
trademarks it so no one else can use it.

Phil

} I still associate microprobe with the scanning electron beam device
} equipped with wavelength spectrometers for the express purpose of x-ray
} microanalysis.
}
} I refer to the little thing used to hold and move objects around as
} micro-manipulators.
}
} I will admit that micro-probe can refer to a lot of things. I wouldn't
} be surprised if the microelectronics folks adopted the term to refer to
} a microscopic test lead. I also suppose the scanning probe microscope
} folks could refer to their tips as microprobes. But to me, a microprobe
} will be those things like ARL used to make.
}
} Maybe that makes me old school, but it seems like a decent working
} definition. I am getting old enough people probably expect me to be a
} bit pig-headed and crotchety anyway. I might as well live up to it. {g}
}
} Warren Straszheim
}
}
} -----Original Message-----
} X-from: edelmare-at-muohio.edu [mailto:edelmare-at-muohio.edu]
} Sent: Wednesday, April 25, 2007 3:44 PM
} To: wesaia-at-iastate.edu
} Subject: [Microscopy] Question of Terminology - "Microprobe"
}
}
} O.k., folks Lets see if the Microscopy and Microanalysis community
} can come an agreement.
}
} Traditionally the term "Microprobe" has been used to refer to a
} dedicated wave length dispersive x-ray microanalysis
} microscope/instrument (XWDS or WDS). Is this still a valid use for
} the the term "Microprobe"? Or is it antiquated?
}
} . . . because it comes into conflict a "newer" use of the word
} "microprobe" as refering to a "small" physical probing device,
} typically mechanical, for manipulating or testing small items. Would
} these probing-manipuating-testing devices be better called
} "Nanoprobes" (even thought they may actually handle items / objects
} in the micrometer to 100's-micrometer range).
}
} Context will NOT sufice to distinguish between the two as
} microscopists now deal with both.
}
} Anyone care to share comments or opinions ?
}
}
} Richard E. Edelmann, Ph.D.
} EXPO Editor, Microscopy and Microanalysis Supplement
} Electron Microscopy Facility Director
} 364 Pearson Hall
} Miami University, Oxford, OH 45056
} Ph: 513.529.5712 Fax: 513.529.4243
} E-mail: edelmare-at-muohio.edu
} http://www.emf.muohio.edu
--
Philip Oshel
Microscopy Facility Supervisor
Biology Department
024C Brooks Hall
Central Michigan University
Mt. Pleasant, MI 48859
voice: (989) 774-3576
dept. fax: (989) 774-3462

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From: opmills-at-mtu.edu
Date: Thu, 26 Apr 2007 09:36:21 -0500
Subject: [Microscopy] wanted old Jeol 4000 TEM camera

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Ellery pretty much captured what my response would be. "Microprobe" by
itself is too generic. The electron microprobe has been, and still is,
called many things. Electron probe, microprobe, electron microprobe, "the"
probe, etc. I have colleagues who even call it "the WDS", but that's a
different problem. I think the "electron microprobe" is the most commonly
used and accepted term for the instrument, at least in the countless number
of reports that included technique descriptions in the geological
literature.

EPMA is a widely accepted acronym, used both for the technique
(microanalysis) and instrument (microanalyzer). I prefer to use it for the
technique and describe the instrument as the electron microprobe.

Jim McGee
************************************
James J. McGee
Materials Engineer
Lockheed Martin
************************************
----- Original Message -----
X-from: {frah0010-at-umn.edu}
To: {mcgeejj-at-kapl.gov}
Sent: Wednesday, April 25, 2007 7:36 PM

All,

Our Gatan 622 SIT camera died. The 4000 is too old to invest in a
new camera or even repair the dead one. I've heard that many 4000's
have been decommissioned, do any of you have the 622 camera or the
wide-angle CCD camera (model 673) you'd sell, trade, donate?

Owen Mills
Michigan Tech Univ.

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From: jgross-at-neuron.uchc.edu
Date: Thu, 26 Apr 2007 13:50:49 -0500
Subject: [Microscopy] Scanners for TEM negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Our lab needs to purchase a new scanner for our TEM negatives. We
have narrowed our choices to either the Epson Perfection V750
(recommended by Keith Young in the May 2006 issue of Microscopy
Today) or the Microtek ScanMaker i900. The major difference between
the two seems to be the "glassless" scanning feature of the Microtek.
Has anyone had first-hand experience of the film scanning ability of
either one of these scanners? Or are there any quirks that would
make one of them less desirable?

Thank you,
Julie Gross
Kent Morest Lab
Dept. of Neuroscience
UCONN Health Center
Farmington, CT 06030
jgross-at-neuron.uchc.edu


==============================Original Headers==============================
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From: mcauliff-at-umdnj.edu
Date: Thu, 26 Apr 2007 14:09:40 -0500
Subject: [Microscopy] Re: Scanners for TEM negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

I solved this problem by putting my negatives, emulsion side up, on
a light box, masking off stray light, and photographing with my digital
camera (3 year old Canon G3) at maximum resolution. I 'invert' the image
with PhotoShop to get a positive and adjust contrast as needed. Works
great and a lot faster than a scanner.

Geoff

jgross-at-neuron.uchc.edu wrote:

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From: ani.issaian-at-csun.edu
Date: Thu, 26 Apr 2007 14:14:29 -0500
Subject: [Microscopy] Re: Scanners for TEM negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

I would recommend the Nikon Coolscan. http://www.nikoncoolscan.com . You
can probably find one for very cheap on ebay or craigslist.
Shawn


--
Shawn Mikula, Ph.D.,
Postdoctoral Scholar
Center for Neuroscience
University of California-Davis,
1544 Newton Court,
Davis, CA 95618,
Phone: 530-754-9209
Fax: 530-754-9136
mail: samikula-at-ucdavis.edu
web: http://brainmaps.org

----- Original Message -----
X-from: {jgross-at-neuron.uchc.edu}
To: {samikula-at-ucdavis.edu}
Sent: Thursday, April 26, 2007 11:58 AM

Julie,
I do not know about these scanners yet I would try them at your local stores
before buying either one, look at the outcome.

Ani


-------------------------------------------------------------------
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From: edelmare-at-muohio.edu
Date: Thu, 26 Apr 2007 14:53:04 -0500
Subject: [Microscopy] Re: Terminology - please vote!

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

O.k. it sounds fairly unamimous that "Electron Microprobe / EPMA" is
the genrally used accepted terminology for a "WDS-Microprobe" and is
better than simply microprobe.

BUT Phil hits the nail on the head with regards to "mechanical
microprobe" type devices.

==} "Let's start using [a term] before some company trademarks it so
no one else can use it."

So what shall it be folks? "Mechanical Microprobe"?
"Nanomanipulator"? Something else?

Let us the microscopists decide before someone trademarks it.

}
} I have to agree with Warren, especially perhaps his last paragraph.
} "Microprobe" has a definite meaning to me and most microscopists.
} I wouldn't suggest using "nanoprobe", as that doesn't really solve
} the problem of confusing terms. Perhaps a simple addition of an
} adjective to make it a noun phrase, like "mechanical microprobe".
} Micromanipulator is a well-known term, so the next step would be
} nanomanipulator. Let's start using that before some company
} trademarks it so no one else can use it.
}
} Phil
}
} } I still associate microprobe with the scanning electron beam device
} } equipped with wavelength spectrometers for the express purpose of x-ray
} } microanalysis.
} }
} } I refer to the little thing used to hold and move objects around as
} } micro-manipulators.
} }
} } I will admit that micro-probe can refer to a lot of things. I wouldn't
} } be surprised if the microelectronics folks adopted the term to refer to
} } a microscopic test lead. I also suppose the scanning probe microscope
} } folks could refer to their tips as microprobes. But to me, a microprobe
} } will be those things like ARL used to make.
} }
} } Maybe that makes me old school, but it seems like a decent working
} } definition. I am getting old enough people probably expect me to be a
} } bit pig-headed and crotchety anyway. I might as well live up to it. {g}
} }
} } Warren Straszheim
} }
} }
} } -----Original Message-----
} } X-from: edelmare-at-muohio.edu [mailto:edelmare-at-muohio.edu]
} } Sent: Wednesday, April 25, 2007 3:44 PM
} } To: wesaia-at-iastate.edu
} } Subject: [Microscopy] Question of Terminology - "Microprobe"
} }
} }
} } O.k., folks Lets see if the Microscopy and Microanalysis community
} } can come an agreement.
} }
} } Traditionally the term "Microprobe" has been used to refer to a
} } dedicated wave length dispersive x-ray microanalysis
} } microscope/instrument (XWDS or WDS). Is this still a valid use for
} } the the term "Microprobe"? Or is it antiquated?
} }
} } . . . because it comes into conflict a "newer" use of the word
} } "microprobe" as refering to a "small" physical probing device,
} } typically mechanical, for manipulating or testing small items. Would
} } these probing-manipuating-testing devices be better called
} } "Nanoprobes" (even thought they may actually handle items / objects
} } in the micrometer to 100's-micrometer range).
} }
} } Context will NOT sufice to distinguish between the two as
} } microscopists now deal with both.
} }
} } Anyone care to share comments or opinions ?
} }
} }
} } Richard E. Edelmann, Ph.D.
} } EXPO Editor, Microscopy and Microanalysis Supplement
} } Electron Microscopy Facility Director
} } 364 Pearson Hall
} } Miami University, Oxford, OH 45056
} } Ph: 513.529.5712 Fax: 513.529.4243
} } E-mail: edelmare-at-muohio.edu
} } http://www.emf.muohio.edu
} --
} Philip Oshel
} Microscopy Facility Supervisor
} Biology Department
} 024C Brooks Hall
} Central Michigan University
} Mt. Pleasant, MI 48859
} voice: (989) 774-3576
} dept. fax: (989) 774-3462
}
} ==============================Original Headers==============================
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Richard E. Edelmann, Ph.D.
EXPO Editor, Microscopy and Microanalysis Supplement
Electron Microscopy Facility Director
364 Pearson Hall
Miami University, Oxford, OH 45056
Ph: 513.529.5712 Fax: 513.529.4243
E-mail: edelmare-at-muohio.edu
http://www.emf.muohio.edu


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From: lcgould-at-med.cornell.edu
Date: Thu, 26 Apr 2007 14:57:27 -0500
Subject: [Microscopy] Re: Scanners for TEM negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Julie,
I have what is now and old Epson Expression 1600 Professional
scanner with trans-illumiator. It works well and is easy. I would
imagine that the newer generation from Epson is also good.
Lee
--
Leona Cohen-Gould, M.S.
Sr. Staff Associate
Director, Electron Microscopy & Histology Core Facility
Manager, Optical Microscopy Core Facility
Weill-Cornell Medical College

voice (212)746-6146
fax (212)746-8175
http://www.cornellcelldevbiology.org
http://www.cornellbiochem.org

==============================Original Headers==============================
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From: Walter.Bobrowski-at-pfizer.com
Date: Thu, 26 Apr 2007 15:05:57 -0500
Subject: [Microscopy] Scanners for TEM negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Microtek i900. Hands down. No questions asked! Great intuitive interface. Been a Microtek fan for years.
Bet regards,
Walt

-----Original Message-----
X-from: jgross-at-neuron.uchc.edu [mailto:jgross-at-neuron.uchc.edu]
Sent: Thursday, April 26, 2007 2:57 PM
To: Bobrowski, Walter

Our lab needs to purchase a new scanner for our TEM negatives. We
have narrowed our choices to either the Epson Perfection V750
(recommended by Keith Young in the May 2006 issue of Microscopy
Today) or the Microtek ScanMaker i900. The major difference between
the two seems to be the "glassless" scanning feature of the Microtek.
Has anyone had first-hand experience of the film scanning ability of
either one of these scanners? Or are there any quirks that would
make one of them less desirable?

Thank you,
Julie Gross
Kent Morest Lab
Dept. of Neuroscience
UCONN Health Center
Farmington, CT 06030
jgross-at-neuron.uchc.edu


==============================Original Headers==============================
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12, 31 -- From Walter.Bobrowski-at-pfizer.com Thu Apr 26 15:05:51 2007
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From: lamiller-at-uiuc.edu
Date: Thu, 26 Apr 2007 15:47:53 -0500
Subject: [Microscopy] Scanners for TEM negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

I have to say I agree, I have a Microtek Scanmaker 9800XL, with a TMA
1600 and I love it. It's the second Microtek I've had, and I'm pretty
pleased by the way it handles TEM negs, once I figured out the best
settings to use with their Silverfast software. Now I love the way it
works.

I do use cut up strips of the neg holders that come with it to tape my
negs across, not directly on the glass face of this scanner, and I
seldom have problems with the "swirls".


Lou Ann


}

--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Lou Ann Miller, MT(ASCP)
Service Supervisor
Center for Microscopic Imaging
College of Veterinary Medicine
Rm 1204 VMBSB
2001 S Lincoln Ave
Urbana, IL 61802

217/244-1567
http://treefrog.cvm.uiuc.edu




Walter.Bobrowski-at-pfizer.com wrote:

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} Microtek i900. Hands down. No questions asked! Great intuitive interface. Been a Microtek fan for years.
} Bet regards,
} Walt
}
}


==============================Original Headers==============================
14, 19 -- From lamiller-at-uiuc.edu Thu Apr 26 15:47:53 2007
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From: donc-at-asmicro.com
Date: Thu, 26 Apr 2007 17:15:08 -0500
Subject: [Microscopy] Re: [a] SEM standards for imaging

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Dear Michael Shaffer,
If what you mean by high magnification could extend to 10Kx and beyond, then
our 292UTC and 150-2DUTC traceable calibration specimens may be suitable for
you. The first one is a 1-dimensional pattern (lines and spaces) with pitch
292 nm. The second one is a 2-dimensional pattern (square grid of bumps)
with 144 nm pitch. Both are available in non-traceable versions at reduced
cost.

Further information is at www.asmicro.com/Supplies/Calibrator_guide.htm,
where you will find information about our full line of sub-micron
calibration specimens.

I hope this information is helpful.

regards,
Don
=============================================
Don Chernoff, Ph.D., President
Advanced Surface Microscopy, Inc. E-Mail: donc-at-asmicro.com
3250 N. Post Rd., Ste. 120 Voice: 317-895-5630
INDIANAPOLIS IN 46226 USA Toll free: 800-374-8557 (in USA & Canada)
web: http://www.asmicro.com Fax: 317-895-5652
[business activities: analytical services in AFM, AFM probes, consulting,
training,
calibration and test specimens, calibration and measurement software,
used NanoScope equipment.]
=============================================
----- Original Message -----
From: michael-at-shaffer.net
To: donc-at-asmicro.com
Sent: Wednesday, April 25, 2007 9:15 AM
Subject: [a] [Microscopy] SEM standards for imaging





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Hello MSA'rs :o)

I need an imaging standard that would allow me to check the magnification
and distortions present for our SEM. A good example is the set of SIRA
gratings, but I thought I'd put it to the list for finding the most
versatile reference standard relative to cost. My needs are (1) to check
magnification in x & y for high and low mag, (2) to check orthogonality at
high and low mag, and (3) to check for barrel, pin-cushioning, or
trapazoidal distortions, at high and low mag ... Where high and low mag
are
} 2000x and {500x.

Tia & cheerios from "the rock" :o)
michael shaffer

SEM/MLA Research Coordinator
{http://www.mun.ca/creait/maf/}
Inco Innovation Centre
Memorial University
St. John's, Newfoundland



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5, 18 -- From: "michael shaffer" {michael-at-shaffer.net}
5, 18 -- To: "MSA Microscopy list" {Microscopy-at-microscopy.com}
5, 18 -- Subject: SEM standards for imaging
5, 18 -- Date: Wed, 25 Apr 2007 10:40:08 -0230
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18, 22 -- From donc-at-asmicro.com Thu Apr 26 17:15:08 2007
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From: dac-at-research.umass.edu
Date: Thu, 26 Apr 2007 19:33:47 -0500
Subject: [Microscopy] Re: Scanners for TEM negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi Julie,

We have the Microtek ScanMaker i900. The glassless holders are indeed a
nice feature. I don't know what size negatives you generate, but I place
the 3.25"x4" negatives "sideways" in the 4"x5" carrier and it works very
well. I scan negatives at 600dpi or 1200dpi. While it does a very nice
job, it is slow - takes just about 5 min to scan a single negative at
the 600dpi setting. I use the USB connection; I tried the FireWire
interface and couldn't get it to work, but put no time into it. The USB
connection does not seem to be the limiting factor. It uses a
"ScanServer" driver to interface with the device so you can switch it on
and off freely without the "Eject USB device" protocol. I do have small
problems at startup sometimes - errors between Adobe Photoshop and the
plugin/device, but powering off the scanner and restarting the
ScanServer fixes it, and once functioning it works w/o error.

When you power on the scanner it goes through some initialization that
lasts ~ 2min; be patient until it is really ready - all noises really
done and the indicator LEDS are steady - or it will hang.

Just to make sure I don't have to adjust for each negative to fit an
8-bit range, I scan at 16-bit with the density range set to 3.0, and
then scale to the actual range and convert to 8-bit when it looks nice
on the monitor for general use, keeping the original scans if warranted
- they are 32Mb as TIFFs....

It does get to be a time-consuming pain scanning a rack of negatives. I
keep a timer set for 5 min and change the negative when done. You can
load 2 negatives at a time in the 4"x5" holder and set it up as 2 jobs,
giving you 10 min break, but that is more than I can keep straight most
days... I sometimes throw 6 negatives at a time on the glass
transparency platen and do the equivalent of a "contact sheet", giving
an even longer interval between feeding loads, but at the peril of glass
platen issues.....

So overall I like it. It seems good and well made for the cost; speed is
the only thing I would change. If anyone knows that I'm doing something
wrong - making it slow - PLEASE tell me!

Hope this helps. Drive up and scan a few if you'd like.

Dale Callaham
Central Microscopy Facility
University of Massachusetts, Amherst.
http://www.bio.umass.edu/microscopy

jgross-at-neuron.uchc.edu wrote:
} ----------------------------------------------------------------------------
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} ----------------------------------------------------------------------------
}
} Our lab needs to purchase a new scanner for our TEM negatives. We
} have narrowed our choices to either the Epson Perfection V750
} (recommended by Keith Young in the May 2006 issue of Microscopy
} Today) or the Microtek ScanMaker i900. The major difference between
} the two seems to be the "glassless" scanning feature of the Microtek.
} Has anyone had first-hand experience of the film scanning ability of
} either one of these scanners? Or are there any quirks that would
} make one of them less desirable?
}
} Thank you,
} Julie Gross
} Kent Morest Lab
} Dept. of Neuroscience
} UCONN Health Center
} Farmington, CT 06030
} jgross-at-neuron.uchc.edu
}
}
} ==============================Original Headers==============================
} 3, 18 -- From jgross-at-neuron.uchc.edu Thu Apr 26 13:50:49 2007
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==============================Original Headers==============================
9, 21 -- From dac-at-research.umass.edu Thu Apr 26 19:33:47 2007
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From: arollins-at-hotmail.com
Date: Thu, 26 Apr 2007 20:44:09 -0500
Subject: [Microscopy] viaWWW: Dehydration of molds

Contents Retrieved from Microscopy Listserver Archives
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This Question/Comment was submitted to the Microscopy Listserver
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Email: arollins-at-hotmail.com
Name: Adena Rollins

Organization: San Joaquin Delta College - Electron Microscopy Program

Title-Subject: [Filtered] Dehydration of molds

Question: I am trying to figure out the best way to dehydrate and dry two types of mold, Rhizopus and A. Niger. I am going to osmium vapour fix them overnight but I would like to know if any of you have any suggestions for the dehydration and drying procedures. I am worried since the samples are so delicate. I am going to be viewing both samples using the SEM.

Thank you...

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==============================Original Headers==============================
7, 11 -- From zaluzec-at-microscopy.com Thu Apr 26 20:44:09 2007
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From: swtkeller-at-yahoo.com
Date: Thu, 26 Apr 2007 20:45:02 -0500
Subject: [Microscopy] viaWWW: TEM-3rd party service providers

Contents Retrieved from Microscopy Listserver Archives
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Email: swtkeller-at-yahoo.com
Name: Sandra Keller

Organization: TA-SICCO

Title-Subject: [Filtered] TEM-3rd party service providers

Question: Hi:
I know this topic comes up on occasion, but I am wanting to tap the extremely valuable resource of this community.

I am looking for the most up-to-date information when it comes to 3rd party service companies. Companies that offer on demand service for JEOL, FEI (Philips), Hitachi, and Zeiss TEM's or any now defunct brands in the US. I am especially interested in information on organizations that offer maintenance (service) contracts, especially for JEOL TEM's.

I have also heard of some type of insurance companies providing some type of similar arrangement, but that was several years ago and I have personally not run across any organization providing this type of service.
Any help on this topic would be greatly appreciated.

Thanks,
Sandra


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From: z0chen09-at-louisville.edu
Date: Thu, 26 Apr 2007 20:45:36 -0500
Subject: [Microscopy] viaWWW: gas injection/heating TEM holder

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Email: z0chen09-at-louisville.edu
Name: Zhiqiang Chen

Organization: University of Louisville

Title-Subject: [Filtered] gas injection/heating TEM holder

Question: Hi, All:
We are looking into buying a gas injection/heating TEM holder. It would be very grateful if you could give some suggestions and recommendation.
Zhiqiang

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From: gary-at-gaugler.com
Date: Thu, 26 Apr 2007 21:44:20 -0500
Subject: [Microscopy] Re: viaWWW: Dehydration of molds

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Yes...a difficult specimen situation. If you
are quick, you do not need to do any fixation.

I did this with Zeiss Supra 55VP at 200V EHT.
This was with the in-lens detector. No coating.

This has to be done fast since the clusters will
implode when subjected to high vacuum. VP is
not all that great. Do HV and quickly.

gary g.


At 05:46 PM 4/26/2007, you wrote:
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From: IHallett-at-hortresearch.co.nz
Date: Thu, 26 Apr 2007 22:21:25 -0500
Subject: [Microscopy] viaWWW: Dehydration of molds

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Adena

One technique I have used successfully in the past is fixing with osmium
vapour, dehydrating using vapor diffusion dehydration and then critical
point drying. This can preserve the conidial structure of Aspergillus
very well. The original reference is:

EJ King and MF Brown 1983 A technique for preserving aerial fungal
structures for scanning electron microscopy. Canadian Journal of
Microbiology 29:653-658

Ian

Ian Hallett
Sensory and Consumer Science - Microscopy
HortResearch, Mt Albert Research Centre
Private Bag 92 169, Auckland Mail Centre
Auckland 1142, New Zealand
+64-9-815 4200 ext 7002

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Email: arollins-at-hotmail.com
Name: Adena Rollins

Organization: San Joaquin Delta College - Electron Microscopy Program

Title-Subject: [Filtered] Dehydration of molds

Question: I am trying to figure out the best way to dehydrate and dry
two types of mold, Rhizopus and A. Niger. I am going to osmium vapour
fix them overnight but I would like to know if any of you have any
suggestions for the dehydration and drying procedures. I am worried
since the samples are so delicate. I am going to be viewing both
samples using the SEM.

Thank you...

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From: keith.morris-at-ucl.ac.uk
Date: Fri, 27 Apr 2007 07:11:58 -0500
Subject: [Microscopy] Scanners for TEM negatives

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Hi Julie,

I don't know if I'm Keith Young, but to be honest Microtek haven't bought
out a new top flight scanner for years and their ArtixScan designs are
living on their old name and hardware. Agfa scanners were simply rebadged
Microtek's until they withdrew from the scanner market along with Fuji. The
Microtek ArtixScan 2500f is pretty much the £5,000 Agfa Duoscan 2550T from 7
years ago, now with firewire instead of SCSI. Not that these professional
Microtek scanners are rubbish, just a bit expensive for a similar scan
quality as the Epson 4990 Photo (and their scans are probably a bit inferior
in resolution to the 6,400dpi Epson V750 - the Agfa 2550T and Epson 4990
are). As I mentioned the upmarket Microtek scanners may have a far better
build quality though. The cheaper Microtek i900, introduced I think in 2004,
has a resolution of about 3,200 dpi. It's glassless design could help reduce
problems with dust, although the scanner optics is no longer 'sealed behind
glass'. It uses 4x5" film holders, a 8x10" glass sandwich or the A4 top bed
for reflective scans. It has been reported as very slow, but then most
prosumer flatbeds at this price aren't that fast. I doubt if you would be
disappointed if you bought the Microtek i900 or the Epson V750 (or the Epson
V700 or 4990 Photo for that matter).

The only way to find out if, at 3,200 dpi quoted resolution, the i900
produces better scans (& faster) than the 6,400 dpi quoted Epson 750 is to
scan the same negative in both, at the same and maximum resolution (I've
never tried the i900, although our Microtek/Agfa Duoscan 2550T looks very
similar). There was also the similar film only Epson F3200 [dpi], that could
scan negatives greater than 9 x 6 cm using 4x5" film holders, but it seems
to have been withdrawn recently.

I did own an old Nikon 2,700 dpi dedicated 35mm slide scanner at home but it
simply took up too much room and it's scan quality was worse than the Canon
9950F I got to replace it, particularly for colour negatives - plus the
Canon only does reflective scans to A4, but annoyingly Canon's Scangear
restricts film sizes to it's film holders. In comparison the V700/V750 pro
can go to A4 for film, with film in holders or just lying on the platen. I
have only used a 6,400 dpi V750 Pro briefly for 35mm colour slide film (my
main interest), and its scan quality was a bit better than my Canon 9950F,
i.e. the fuzz was a tiny tiny bit sharper, it's not streets ahead at all
(although it's Epson Scan twain interface was in another league). Plus the
35mm slide holder retaining clips on the V750 are rather flimsy (although
the Canon and Epson 4990 don't even bother with retaining clips, using
gravity to hold them in place). I don't know how good the 35mm clips on the
i900 are (they don't look great either). At work our 4,800 dpi Epson 4990
Photo is more than adequate for 1,200 dpi B&W TEM film scans, so I haven’t
bothered upgrading to a V750 Pro. The V750 does also offer an optional
fluid mount scan accessory like every expensive drum scanners, but that’s
unlikely to be of interest for TEM film scanning. It's meant to get rid of
Newton rings (swirls) and can assist in hiding scratches and dust, but it
often introduces bubbles instead.

However you will get superior scans from an £8,000 Hasselblad 8,000 dpi
[Imacon] 848 semi-drum scanner, but often it will be the film grain that
looks a bit better resolved rather than actual image detail. Plus you must
use the film holders - it scans fast though. It also has no glass between
the film and detector. Things like FARE/ICE dust removal and accurate colour
reproduction (the latter being essential for professionals that need correct
skin tones or accurate reproductions of museum articles) are irrelevant for
your B&W scientific images.

The excellent 4000 dpi 35mm Nikon Coolscan 9000 [3-CCD sensor] film scanner
comes in at £2,000. However the Nikon 9000 can only scan film up to 9 x 6 cm
in size and histological sections on glass slides (too small for most TEM
negatives unless you cut them down). Plus it has a lot of software/hardware
for 35mm colour film thrown in you probably won't need.

To be honest the 4,800 dpi Epson 4990 Photo at £250 is more than adequate
for large format negatives (TEM film) as it can go up to A4 film (six TEM
negatives per scan) and Epson's Scan is an easier Twain interface than
Silverfast and Canons awful Scangear (there is also the highly regarded
Vuescan third party twain software available).

In practice it is most unlikely that will often want to scan at more than
1,200 dpi anyway as the resulting file size will be enormous and highly
prone to file corruption on the PC (but images should have noticeably better
resolution if scanned at 2,400dpi). Most scan just for publication or for PC
on-screen image analysis, rather than printing to A4/A3. A Epson 4990 Photo
4,800 dpi scan of Kodak 4489 negative is around 250 Mb in TIF format, at
2,400 dpi it drops to a 60Mb TIF file with little different in image
quality. There no reason however not to go for the better 6,400 dpi Epson
V750 Pro, even if you scan mainly at 1,200 dpi, as it's only a bit more
money (and not ours). The 6,400 dpi will be useful for enlargement of
selected areas (scanning at 3,200 dpi being optimal).

Perhaps one downside to the V750 Pro is that it works best with the
slide/film holders and their little leg supports. Some sizes of TEM film may
have small parts of the image hidden by a 4x5" film holder. You can source
third party film holders though (see Doug Fisher), or you can just drop them
onto the platen and live with a possible small drop in resolution. As
mentioned you can get interference patterns (swirls) if the negative is
placed on the platen rather than using the 4x5" film holder. This is
probably caused by a slightly damp negative (high humidity) or the glass
platen having greasy finger marks. So far I have always got rid of this by
cleaning the platen (50% propanol/50% water with soft tissue and air-bulb
blow dry - also great for finger smudged VDU screens). Remove film from the
platen with a sheet of card rather than fingers (i.e. never touch the glass
platen). No-one here ever bothers to use the Epson 4990's 4x5" film holders
as it obscures part of the negative, only takes a few films and is far more
fiddly. They just place six TEM negatives directly on the platen (correct
side up).

If you are really really serious about scanning film for some reason there
is also the likes of professional flatbed scanners such as the Kodak
‘Creo’£15k [10,000 dpi] IQSmart 3, the £30k [8000 to 14000 dpi] EverSmart
Supreme II flatbeds (www.kodak.com). However cheaper consumer ‘photo’ flat
beds such as the new 6,400 dpi Epson V750 and V750 Pro come in at £500 and
£650 respectively, and I can't see any reason to spend more for infrequent
scans of large format B&W film, as you will rarely, if ever, scan at maximum
resolution. They also have convenient USB2 and Firewire interfaces and work
with Apples or PCs.

You will have to spend a bit of time working on the best twain scan settings
and images will probably need some post-editing in Photoshop CS3 to get
optimal scanned image quality.

But the choice is yours. Do however have a look at
http://www.photo-i.co.uk for Independent reviews of some prosumer large
format (A4) film scanners (not the i900). Also note that these cheaper
scanners are for light use, if you want to scan hundreds of films a day, and
not be chained to the scanner, look elsewhere and with a deeper pocket.

Regards

Keith

PS. My 'Scanning film on a budget' Microscopy Today article has been updated
and reprinted in Infocus (March 2007) the UK Royal Microscopical society's
magazine. I can't send a pdf though as the editor hasn't passed on a
corrected version yet. I can only send a scan of the article taken using my
home 4,800 dpi Canon 9950F (scanned at 600 dpi) - but don't try that at home
with your £2,000 Nikon Coolscan 9000.

PPS. As mentioned the now withdrawn Canon 9550F has a terrible twain
software interface(Scangear), the Epsons Scan one is miles better, so I
would avoid the Canon even if you can still find it [unless its only ever
being used for scanning photographs or with standard film holder sizes].
Interestingly Canon scrapped their dedicated 35mm film scanners for the
9950F (and they should know something about film photography) but the poor
Scangear twain interface didn't make many friends. I bought the 9950F just
before the Epson 4990 Photo came in - which I later purchased for work use,
mainly for TEM negatives, 2D gel film and reflective scans.


---------------------------
Dr Keith J Morris
Imaging Facilities Manager
Cell Biology
Institute of Ophthalmology
UCL, London EC1V 9EL





-----Original Message-----
X-from: jgross-at-neuron.uchc.edu [mailto:jgross-at-neuron.uchc.edu]
Sent: 26 April 2007 19:55
To: keith.morris-at-ucl.ac.uk

Our lab needs to purchase a new scanner for our TEM negatives. We
have narrowed our choices to either the Epson Perfection V750
(recommended by Keith Young in the May 2006 issue of Microscopy
Today) or the Microtek ScanMaker i900. The major difference between
the two seems to be the "glassless" scanning feature of the Microtek.
Has anyone had first-hand experience of the film scanning ability of
either one of these scanners? Or are there any quirks that would
make one of them less desirable?

Thank you,
Julie Gross
Kent Morest Lab
Dept. of Neuroscience
UCONN Health Center
Farmington, CT 06030
jgross-at-neuron.uchc.edu




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From: frank.karl-at-degussa.com
Date: Fri, 27 Apr 2007 07:32:24 -0500
Subject: [Microscopy] Terminology - please vote!

Contents Retrieved from Microscopy Listserver Archives
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What an interesting idea! I like MM, oh wait, Disney has that locked up!

While we are on the subject, can we arrange to get people to stop using
"electron microscope" when they mean transmission electron microscope or
scanning electron microscope?


Oh!, If I was king of the world................



edelmare-at-muohio.e
du To: frank.karl-at-degussa.com
cc:
04/26/2007 03:54 Subject: [Microscopy] Re: Terminology - please vote!
PM
Please respond to
edelmare








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O.k. it sounds fairly unamimous that "Electron Microprobe / EPMA" is
the genrally used accepted terminology for a "WDS-Microprobe" and is
better than simply microprobe.

BUT Phil hits the nail on the head with regards to "mechanical
microprobe" type devices.

==} "Let's start using [a term] before some company trademarks it so
no one else can use it."

So what shall it be folks? "Mechanical Microprobe"?
"Nanomanipulator"? Something else?

Let us the microscopists decide before someone trademarks it.

}
} I have to agree with Warren, especially perhaps his last paragraph.
} "Microprobe" has a definite meaning to me and most microscopists.
} I wouldn't suggest using "nanoprobe", as that doesn't really solve
} the problem of confusing terms. Perhaps a simple addition of an
} adjective to make it a noun phrase, like "mechanical microprobe".
} Micromanipulator is a well-known term, so the next step would be
} nanomanipulator. Let's start using that before some company
} trademarks it so no one else can use it.
}
} Phil
}
} } I still associate microprobe with the scanning electron beam device
} } equipped with wavelength spectrometers for the express purpose of x-ray
} } microanalysis.
} }
} } I refer to the little thing used to hold and move objects around as
} } micro-manipulators.
} }
} } I will admit that micro-probe can refer to a lot of things. I wouldn't
} } be surprised if the microelectronics folks adopted the term to refer to
} } a microscopic test lead. I also suppose the scanning probe microscope
} } folks could refer to their tips as microprobes. But to me, a microprobe
} } will be those things like ARL used to make.
} }
} } Maybe that makes me old school, but it seems like a decent working
} } definition. I am getting old enough people probably expect me to be a
} } bit pig-headed and crotchety anyway. I might as well live up to it. {g}
} }
} } Warren Straszheim
} }
} }
} } -----Original Message-----
} } X-from: edelmare-at-muohio.edu [mailto:edelmare-at-muohio.edu]
} } Sent: Wednesday, April 25, 2007 3:44 PM
} } To: wesaia-at-iastate.edu
} } Subject: [Microscopy] Question of Terminology - "Microprobe"
} }
} }
} } O.k., folks Lets see if the Microscopy and Microanalysis community
} } can come an agreement.
} }
} } Traditionally the term "Microprobe" has been used to refer to a
} } dedicated wave length dispersive x-ray microanalysis
} } microscope/instrument (XWDS or WDS). Is this still a valid use for
} } the the term "Microprobe"? Or is it antiquated?
} }
} } . . . because it comes into conflict a "newer" use of the word
} } "microprobe" as refering to a "small" physical probing device,
} } typically mechanical, for manipulating or testing small items. Would
} } these probing-manipuating-testing devices be better called
} } "Nanoprobes" (even thought they may actually handle items / objects
} } in the micrometer to 100's-micrometer range).
} }
} } Context will NOT sufice to distinguish between the two as
} } microscopists now deal with both.
} }
} } Anyone care to share comments or opinions ?
} }
} }
} } Richard E. Edelmann, Ph.D.
} } EXPO Editor, Microscopy and Microanalysis Supplement
} } Electron Microscopy Facility Director
} } 364 Pearson Hall
} } Miami University, Oxford, OH 45056
} } Ph: 513.529.5712 Fax: 513.529.4243
} } E-mail: edelmare-at-muohio.edu
} } http://www.emf.muohio.edu
} --
} Philip Oshel
} Microscopy Facility Supervisor
} Biology Department
} 024C Brooks Hall
} Central Michigan University
} Mt. Pleasant, MI 48859
} voice: (989) 774-3576
} dept. fax: (989) 774-3462
}
} ==============================Original
Headers==============================
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} 3, 22 -- Date: Thu, 26 Apr 2007 08:56:55 -0400
} 3, 22 -- To: Microscopy-at-microscopy.com
} 3, 22 -- From: Philip Oshel {oshel1pe-at-cmich.edu}
} 3, 22 -- Subject: [Microscopy] RE: Question of Terminology - "Microprobe"
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Richard E. Edelmann, Ph.D.
EXPO Editor, Microscopy and Microanalysis Supplement
Electron Microscopy Facility Director
364 Pearson Hall
Miami University, Oxford, OH 45056
Ph: 513.529.5712 Fax: 513.529.4243
E-mail: edelmare-at-muohio.edu
http://www.emf.muohio.edu


==============================Original
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From: USTweety-at-hotmail.com
Date: Fri, 27 Apr 2007 07:38:17 -0500
Subject: [Microscopy] viaWWW: desktop microscopist

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

This Question/Comment was submitted to the Microscopy Listserver
using the WWW based Form at http://www.microscopy.org/MicroscopyListserver/MLFormMail.html
---------------------------------------------------------------------------
Remember this posting is most likely not from a Subscriber, so when replying
please copy both USTweety-at-hotmail.com as well as the MIcroscopy Listserver
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Email: USTweety-at-hotmail.com
Name: Marla Tchechov

Title-Subject: [Filtered] desktop microscopist

Question: I want yo buy a software called desktop microscopist. Where can I get this?

---------------------------------------------------------------------------

==============================Original Headers==============================
5, 11 -- From zaluzec-at-microscopy.com Fri Apr 27 07:38:17 2007
5, 11 -- Received: from [206.69.208.22] (mac22.zaluzec.com [206.69.208.22])
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5, 11 -- From: USTweety-at-hotmail.com (by way of MicroscopyListserver)
5, 11 -- Subject: viaWWW: desktop microscopist
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From: eschumacher-at-mccrone.com
Date: Fri, 27 Apr 2007 08:00:55 -0500
Subject: [Microscopy] Short Course Announcement: Optical Crystallography

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Fellow Listers,

Learn how Optical Crystallography can help you to further characterize
samples in forensics, soil science, pharmaceuticals, environmental
analyses, and earth sciences. Optical crystallography can be one of the
most challenging topics for the polarized light microscopist to
understand, but when mastered and applied to crystalline specimens,
becomes a powerful tool for materials analysis.

The following courses will be held this summer at the College of
Microscopy located in Westmont IL;

COM160 Techniques of Optical Crystallography: Crystal Identification
using the Polarized Light Microscope, July 16-20, 2007.

COM170 Universal Stage Methods for the Study of Crystalline Materials,
August 20-22, 2007.

COM460 Identification of Opaque Minerals Using Reflected Light
Microscopy, August 15-17, 2007.

Each of these courses is taught by Dan Kile, a leading authority in
Optical Crystallography and one of the College's adjunct professors.

For more detailed information about this course or to sign up please
visit our website at www.collegeofmicroscopy.com or call Tricia Bevill,
Registrar, at 630-887-7100.

College of Microscopy, 850 Pasquinelli Drive, Westmont, IL 60559-5539




Elaine Schumacher
Senior Research Scientist
McCrone Associates, Inc.
850 Pasquinelli Drive
Westmont, IL 60559-5539 USA
630-887-7100 (tel)
630-887-7417 (fax)
E-mail: eschumacher-at-mccrone.com
Web Site: www.mccrone.com


==============================Original Headers==============================
7, 27 -- From eschumacher-at-mccrone.com Fri Apr 27 08:00:55 2007
7, 27 -- Received: from pgp.mccrone.com (McCrone-Associates-1051626.cust-rtr.ameritech.net [68.23.63.122] (may be forged))
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From: gcouger-at-science-info.net
Date: Fri, 27 Apr 2007 10:40:19 -0500
Subject: [Microscopy] Re: 2nd for posting to the list

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Bill, Gary & the list,

I looked in the headers of the out of offices messages are sent
directly to me and the list. Nestor has no control over that. Nestor
does a very good job scrubbing the list to stop them from going out to
the list but he has no way to stop the first one from going back to
people that post to the list.

He could take parasitics action a Yahoo does and not mail any more
messages out to anyone that bounces a message for any reason back to the
list but most people don't think that the right way to handle a
professional list. Having to delete a half dozen emails is not going to
traumatize any of us.

Even Yahoo in its Draconian ways hasn't done away this problem as you
still get the messages bounce back to you the first time there is a
problem with a email delivery for any reason or there is an out of
office message.

Compared to other list Nestor runs a very good one that is a great
service to microscopist all over the world.

Being a Monday morning quarter back on how to run a list is easy but
running a list as big as this one isn't. Some of the organizations we
work for require that we have the out of office messages and not access
private email on the clock. So those of use that work there don't have
much choice in the matter.

Gordon Couger
www.science-info.net
Repository of old microscope documentation

tivol-at-caltech.edu wrote:
} On Apr 20, 2007, at 6:49 PM, gary-at-gaugler.com wrote:
}
}
} } The reason NOT to post to the list is that you get
} } volumes of "Out Of Office" messages. This is the
} } same as when you make a new posting. Most of the
} } defunct messages are trapped by Eudora but quite
} } a few still get though....sigh.
} }
} } Some do not have this subject but say that they
} } are gone from xx to yy.
} }
} }
} Dear Gary,
} Is it possible to have all OOO messages have the subject line be "Out
} Of Office"? If so, Nestor could request it, but if the company that
} one works for has a standard OOO heading, that may be impractical.
} Yours,
} Bill Tivol, PhD
} EM Scientist
} Electron Cryo-Microscopy Facility
} Broad Center, Mail Code 114-96
} California Institute of Technology
} Pasadena CA 91125
} (626) 395-8833
} tivol-at-caltech.edu
}
}


==============================Original Headers==============================
9, 20 -- From gcouger-at-science-info.net Fri Apr 27 10:40:19 2007
9, 20 -- Received: from smtp101.biz.mail.mud.yahoo.com (smtp101.biz.mail.mud.yahoo.com [68.142.200.236])
9, 20 -- by ns.microscopy.com (8.12.11.20060308/8.12.8) with SMTP id l3RFeJDX000463
9, 20 -- for {microscopy-at-microscopy.com} ; Fri, 27 Apr 2007 10:40:19 -0500
9, 20 -- Received: (qmail 37059 invoked from network); 27 Apr 2007 15:40:18 -0000
9, 20 -- Received: from unknown (HELO ?192.168.1.100?) (gcouger-at-science-info.net-at-74.195.225.38 with plain)
9, 20 -- by smtp101.biz.mail.mud.yahoo.com with SMTP; 27 Apr 2007 15:40:18 -0000
9, 20 -- X-YMail-OSG: ENMo0JAVM1nurTJc_wB5DtX8KCVq7T154qsHGgrSvpGCLz0a7mu55.edjOrXBKjHRBqINo4LBAJgD8T0QIgH29Vu7eh6RdpRaNEN2HhxTZnturqIKN0-
9, 20 -- Message-ID: {46321967.4090305-at-science-info.net}
9, 20 -- Date: Fri, 27 Apr 2007 10:40:23 -0500
9, 20 -- From: Gordon Couger {gcouger-at-science-info.net}
9, 20 -- User-Agent: Thunderbird 1.5.0.10 (Macintosh/20070221)
9, 20 -- MIME-Version: 1.0
9, 20 -- To: tivol-at-caltech.edu, microscopy-at-microscopy.com,
9, 20 -- Gary Gaugler {gary-at-gaugler.com}
9, 20 -- Subject: Re: [Microscopy] 2nd for posting to the list
9, 20 -- References: {200704231643.l3NGhemP006693-at-ns.microscopy.com}
9, 20 -- In-Reply-To: {200704231643.l3NGhemP006693-at-ns.microscopy.com}
9, 20 -- Content-Type: text/plain; charset=ISO-8859-1; format=flowed
9, 20 -- Content-Transfer-Encoding: 7bit
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From: TindallR-at-missouri.edu
Date: Fri, 27 Apr 2007 10:51:10 -0500
Subject: [Microscopy] Re: 2nd for posting to the list

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi all,

I have to agree 100% on this. When I post to this list I may get 4-6
"out of office" replies. Big whoop.

I an unendingly puzzled as to why this is such a big issue.

Randy

-----Original Message-----
X-from: gcouger-at-science-info.net [mailto:gcouger-at-science-info.net]
Sent: Friday, April 27, 2007 10:42 AM
To: Tindall, Randy D.

Bill, Gary & the list,

I looked in the headers of the out of offices messages are sent
directly to me and the list. Nestor has no control over that. Nestor
does a very good job scrubbing the list to stop them from going out to
the list but he has no way to stop the first one from going back to
people that post to the list.

He could take parasitics action a Yahoo does and not mail any more
messages out to anyone that bounces a message for any reason back to the
list but most people don't think that the right way to handle a
professional list. Having to delete a half dozen emails is not going to
traumatize any of us.

Even Yahoo in its Draconian ways hasn't done away this problem as you
still get the messages bounce back to you the first time there is a
problem with a email delivery for any reason or there is an out of
office message.

Compared to other list Nestor runs a very good one that is a great
service to microscopist all over the world.

Being a Monday morning quarter back on how to run a list is easy but
running a list as big as this one isn't. Some of the organizations we
work for require that we have the out of office messages and not access
private email on the clock. So those of use that work there don't have
much choice in the matter.

Gordon Couger
www.science-info.net
Repository of old microscope documentation

tivol-at-caltech.edu wrote:
} On Apr 20, 2007, at 6:49 PM, gary-at-gaugler.com wrote:
}
}
} } The reason NOT to post to the list is that you get volumes of "Out Of

} } Office" messages. This is the same as when you make a new posting.
} } Most of the defunct messages are trapped by Eudora but quite a few
} } still get though....sigh.
} }
} } Some do not have this subject but say that they are gone from xx to
} } yy.
} }
} }
} Dear Gary,
} Is it possible to have all OOO messages have the subject line be
"Out
} Of Office"? If so, Nestor could request it, but if the company that
} one works for has a standard OOO heading, that may be impractical.
} Yours,
} Bill Tivol, PhD
} EM Scientist
} Electron Cryo-Microscopy Facility
} Broad Center, Mail Code 114-96
} California Institute of Technology
} Pasadena CA 91125
} (626) 395-8833
} tivol-at-caltech.edu
}
}


==============================Original
Headers==============================
9, 20 -- From gcouger-at-science-info.net Fri Apr 27 10:40:19 2007 9, 20 --
Received: from smtp101.biz.mail.mud.yahoo.com
(smtp101.biz.mail.mud.yahoo.com [68.142.200.236])
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id l3RFeJDX000463
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9, 20 -- Message-ID: {46321967.4090305-at-science-info.net}
9, 20 -- Date: Fri, 27 Apr 2007 10:40:23 -0500 9, 20 -- From: Gordon
Couger {gcouger-at-science-info.net} 9, 20 -- User-Agent: Thunderbird
1.5.0.10 (Macintosh/20070221) 9, 20 -- MIME-Version: 1.0 9, 20 -- To:
tivol-at-caltech.edu, microscopy-at-microscopy.com,
9, 20 -- Gary Gaugler {gary-at-gaugler.com}
9, 20 -- Subject: Re: [Microscopy] 2nd for posting to the list 9, 20 --
References: {200704231643.l3NGhemP006693-at-ns.microscopy.com}
9, 20 -- In-Reply-To: {200704231643.l3NGhemP006693-at-ns.microscopy.com}
9, 20 -- Content-Type: text/plain; charset=ISO-8859-1; format=flowed 9,
20 -- Content-Transfer-Encoding: 7bit ==============================End
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==============================Original Headers==============================
21, 25 -- From TindallR-at-missouri.edu Fri Apr 27 10:51:10 2007
21, 25 -- Received: from um-tsmtpout1.um.umsystem.edu (um-tsmtpout1.um.umsystem.edu [209.106.228.23])
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21, 25 -- Subject: RE: [Microscopy] Re: 2nd for posting to the list
21, 25 -- Date: Fri, 27 Apr 2007 10:51:08 -0500
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21, 25 -- References: {200704271542.l3RFgGVW002515-at-ns.microscopy.com}
21, 25 -- From: "Tindall, Randy D." {TindallR-at-missouri.edu}
21, 25 -- To: {microscopy-at-microscopy.com}
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From: g-leser-at-northwestern.edu
Date: Fri, 27 Apr 2007 11:32:51 -0500
Subject: [Microscopy] nearest neighbor analysis

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html


Hi,

Is there any software available that will allow the calculation of pair correlation function from sets of x,y coordinates? I have a number of electron micrographs with colloidal gold staining and I would like to do an analysis of particle distribution for single and double labeling. Is there a way to do this with image J?

Thanks.

George


George P. Leser, PhD
Dept. Biochemistry, Molecular Biology, and Cell Biology
Northwestern University
Hogan 2-100
2153 North Campus Drive
Evanston, IL 60208

g-leser-at-northwestern.edu



==============================Original Headers==============================
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From: tivol-at-caltech.edu
Date: Fri, 27 Apr 2007 12:02:38 -0500
Subject: [Microscopy] Re: Terminology - please vote!

Contents Retrieved from Microscopy Listserver Archives
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http://wbgn013.biozentrum.uni-wuerzburg.de/ImageJ/two-point-correlation.html



--
Shawn Mikula, Ph.D.,
Postdoctoral Scholar
Center for Neuroscience
University of California-Davis,
1544 Newton Court,
Davis, CA 95618,
Phone: 530-754-9209
Fax: 530-754-9136
mail: samikula-at-ucdavis.edu
web: http://brainmaps.org

----- Original Message -----
X-from: {g-leser-at-northwestern.edu}
To: {samikula-at-ucdavis.edu}
Sent: Friday, April 27, 2007 9:39 AM


On Apr 27, 2007, at 5:32 AM, frank.karl-at-degussa.com wrote:

} While we are on the subject, can we arrange to get people to stop using
} "electron microscope" when they mean transmission electron microscope
} or
} scanning electron microscope?
}
Dear Frank,
Maybe we could restrict "electron microscope" to those instruments
with both capabilities; it's better than referring to them as
scanning/transmission electron microscopes. If the instruments are
designed for cryo, the designation "scanning/transmission electron
cryo-microscopes" is almost Germanic.
Yours,
Bill Tivol, PhD
EM Scientist
Electron Cryo-Microscopy Facility
Broad Center, Mail Code 114-96
California Institute of Technology
Pasadena CA 91125
(626) 395-8833
tivol-at-caltech.edu


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From: dac-at-research.umass.edu
Date: Fri, 27 Apr 2007 15:36:14 -0500
Subject: [Microscopy] Scanners for TEM negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Hi -

If it is any use to people interested in "budget" scanners, I have
posted an image on my webspace. It is an image of an unknown bacterium
shot at 15kX on a JEOL JEM-100s on Kodak 4489 and scanned in the
Microtek i900 at 1200 dpi. It was scanned at 16 bits and scaled to an
8bit range and converted to JPG. The jpg loses a bit of quality, but not
much.

http://www-unix.oit.umass.edu/~dac/temp/05479_15k_1200dpi.jpg

BTW, if anyone knows this beast, please let me know what it is. It is
growing in crashing non-sterile Chlamydomonas cultures (which I raise
under a fluorescent lamp in the lab for interesting test samples....)

Cheers!

Dale Callaham
UMASS Amherst


} -----Original Message-----
} X-from: jgross-at-neuron.uchc.edu [mailto:jgross-at-neuron.uchc.edu]
} Sent: 26 April 2007 19:55
} To: keith.morris-at-ucl.ac.uk
} Subject: [Microscopy] Scanners for TEM negatives
}
}
}
}
} ----------------------------------------------------------------------------
} The Microscopy ListServer -- CoSponsor: The Microscopy Society of America
} To Subscribe/Unsubscribe -- http://www.microscopy.com/MicroscopyListserver
} On-Line Help http://www.microscopy.com/MicroscopyListserver/FAQ.html
} ----------------------------------------------------------------------------
}
} Our lab needs to purchase a new scanner for our TEM negatives. We
} have narrowed our choices to either the Epson Perfection V750
} (recommended by Keith Young in the May 2006 issue of Microscopy
} Today) or the Microtek ScanMaker i900. The major difference between
} the two seems to be the "glassless" scanning feature of the Microtek.
} Has anyone had first-hand experience of the film scanning ability of
} either one of these scanners? Or are there any quirks that would
} make one of them less desirable?
}
} Thank you,
} Julie Gross
} Kent Morest Lab
} Dept. of Neuroscience
} UCONN Health Center
} Farmington, CT 06030
} jgross-at-neuron.uchc.edu
}
}
}

==============================Original Headers==============================
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From: joswiak-at-astro.washington.edu
Date: Fri, 27 Apr 2007 16:08:32 -0500
Subject: [Microscopy] TEM specialist job

Contents Retrieved from Microscopy Listserver Archives
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I am posting this job description for a colleague. Please respond to the
Center for Nanotechnology listed below if you are interested in this
position.


} Research Scientist 3 position at the University of Washigton
}
}
}
}
} Position Description:
}
} This is a 100% position. The Research Scientist will act as a scientific
} liaison and provide technical support to users of the University of
} Washington Nanotech User Facility (NTUF), a node of the National
} Nanotechnology Infrastructure Network (NNIN). The successful candidate
} will
} develop protocols on various state-of-the-art electron microscopy tools to
} address demand from internal and external users and will develop new
} capabilities and applications using existing equipment. This position has
} potential to evolve into a managerial position upon future evaluation.
} Responsibilities include:
} . To act as a technical lead with a focus on transmission electron
} microscopy (TEM) in support of research projects for NTUF users across the
} nation.
} . To enhance the capabilities of existing electron microscopy tools
} and
} explores new and emerging applications of these tools with the goal of
} increasing NTUF usage.
} . To design creative training procedures and ensure effective training
} of NTUF users on the use of TEM and other NTUF tools.
} . To develop and formulate sample preparation procedures in support of
} users.
} . To perform routine operation and maintenance on the TEM and other
} NTUF
} equipment
} . To perform contract work for remote users nationwide
} . To collaborate with and lead tasks/projects with other NTUF
} personnel
} in order to achieve objectives and/or enhance service quality
} . To assume other duties as requested by the directors and lab
} manager.
}
}
}
}
}
}
} Requirements:
}
} The successful candidate is expected to have a broad knowledge of the
} principle and practice of transmission electron microscopy and to
} establishtechnical expertise in TEM operation, working proactively and
} collaboratively with a vibrant scientific community making use of NTUF and
} NNIN.
} . Education: Ph.D. in Science or Engineering with 1-2 years of
} professional experience or BS/MS level with 3-5 years of relevant
} experience
}
} . Broad knowledge of nanoscience and nanotechnology tools and
} applications
} . Research experience in the field of TEM applications in nanoscale
} science and technology, preferably in bio-related
} . Experience in working with students/users in a multi-user academic
} facility
} . Excellent written and communication skills for preparation of
} reports
} and presentations
} . Self motivated with a strong desire to succeed
} . Excellent team player who will contribute to the team success
}
}
}
}
}
} ---------------------------------------------------------------
}
} Dong Qin, PhD MBA
}
} Associate Director, Center for Nanotechnology
}
} University of Washington, Seattle, WA 98195
}
} Voice: 206-616-2118; Fax: 206-221-2528
}
} {http://depts.washington.edu/ntuf} http://depts.washington.edu/ntuf
}
} www.nano.washington.edu
}
}
}
}
}
}


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From: jfactor-at-ns.purchase.edu
Date: Fri, 27 Apr 2007 19:02:34 -0500
Subject: [Microscopy] Scanners for TEM negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

A veritable treatise on scanners. Thank you. I love this list!
--Jan Factor

----------------------------------------------
Jan Robert Factor, Ph.D.
Professor of Biology
----------------------------------------------
Natural Science Bldg.
Purchase College, State University of New York
735 Anderson Hill Rd.
Purchase, NY 10577
USA
----------------------------------------------
Office Tel: 914-251-6659
Office Fax: 914-251-6635
E-mail: jfactor-at-ns.purchase.edu
----------------------------------------------


keith.morris-at-ucl.ac.uk wrote:
} ----------------------------------------------------------------------------
} The Microscopy ListServer -- CoSponsor: The Microscopy Society of America
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} ----------------------------------------------------------------------------
}
} Hi Julie,
}
} I don't know if I'm Keith Young, but to be honest Microtek haven't bought
} out a new top flight scanner for years and their ArtixScan designs are
} living on their old name and hardware. Agfa scanners were simply rebadged
} Microtek's until they withdrew from the scanner market along with Fuji. The
} Microtek ArtixScan 2500f is pretty much the £5,000 Agfa Duoscan 2550T from 7
} years ago, now with firewire instead of SCSI. Not that these professional
} Microtek scanners are rubbish, just a bit expensive for a similar scan
} quality as the Epson 4990 Photo (and their scans are probably a bit inferior
} in resolution to the 6,400dpi Epson V750 - the Agfa 2550T and Epson 4990
} are). As I mentioned the upmarket Microtek scanners may have a far better
} build quality though. The cheaper Microtek i900, introduced I think in 2004,
} has a resolution of about 3,200 dpi. It's glassless design could help reduce
} problems with dust, although the scanner optics is no longer 'sealed behind
} glass'. It uses 4x5" film holders, a 8x10" glass sandwich or the A4 top bed
} for reflective scans. It has been reported as very slow, but then most
} prosumer flatbeds at this price aren't that fast. I doubt if you would be
} disappointed if you bought the Microtek i900 or the Epson V750 (or the Epson
} V700 or 4990 Photo for that matter).
}
} The only way to find out if, at 3,200 dpi quoted resolution, the i900
} produces better scans (& faster) than the 6,400 dpi quoted Epson 750 is to
} scan the same negative in both, at the same and maximum resolution (I've
} never tried the i900, although our Microtek/Agfa Duoscan 2550T looks very
} similar). There was also the similar film only Epson F3200 [dpi], that could
} scan negatives greater than 9 x 6 cm using 4x5" film holders, but it seems
} to have been withdrawn recently.
}
} I did own an old Nikon 2,700 dpi dedicated 35mm slide scanner at home but it
} simply took up too much room and it's scan quality was worse than the Canon
} 9950F I got to replace it, particularly for colour negatives - plus the
} Canon only does reflective scans to A4, but annoyingly Canon's Scangear
} restricts film sizes to it's film holders. In comparison the V700/V750 pro
} can go to A4 for film, with film in holders or just lying on the platen. I
} have only used a 6,400 dpi V750 Pro briefly for 35mm colour slide film (my
} main interest), and its scan quality was a bit better than my Canon 9950F,
} i.e. the fuzz was a tiny tiny bit sharper, it's not streets ahead at all
} (although it's Epson Scan twain interface was in another league). Plus the
} 35mm slide holder retaining clips on the V750 are rather flimsy (although
} the Canon and Epson 4990 don't even bother with retaining clips, using
} gravity to hold them in place). I don't know how good the 35mm clips on the
} i900 are (they don't look great either). At work our 4,800 dpi Epson 4990
} Photo is more than adequate for 1,200 dpi B&W TEM film scans, so I haven’t
} bothered upgrading to a V750 Pro. The V750 does also offer an optional
} fluid mount scan accessory like every expensive drum scanners, but that’s
} unlikely to be of interest for TEM film scanning. It's meant to get rid of
} Newton rings (swirls) and can assist in hiding scratches and dust, but it
} often introduces bubbles instead.
}
} However you will get superior scans from an £8,000 Hasselblad 8,000 dpi
} [Imacon] 848 semi-drum scanner, but often it will be the film grain that
} looks a bit better resolved rather than actual image detail. Plus you must
} use the film holders - it scans fast though. It also has no glass between
} the film and detector. Things like FARE/ICE dust removal and accurate colour
} reproduction (the latter being essential for professionals that need correct
} skin tones or accurate reproductions of museum articles) are irrelevant for
} your B&W scientific images.
}
} The excellent 4000 dpi 35mm Nikon Coolscan 9000 [3-CCD sensor] film scanner
} comes in at £2,000. However the Nikon 9000 can only scan film up to 9 x 6 cm
} in size and histological sections on glass slides (too small for most TEM
} negatives unless you cut them down). Plus it has a lot of software/hardware
} for 35mm colour film thrown in you probably won't need.
}
} To be honest the 4,800 dpi Epson 4990 Photo at £250 is more than adequate
} for large format negatives (TEM film) as it can go up to A4 film (six TEM
} negatives per scan) and Epson's Scan is an easier Twain interface than
} Silverfast and Canons awful Scangear (there is also the highly regarded
} Vuescan third party twain software available).
}
} In practice it is most unlikely that will often want to scan at more than
} 1,200 dpi anyway as the resulting file size will be enormous and highly
} prone to file corruption on the PC (but images should have noticeably better
} resolution if scanned at 2,400dpi). Most scan just for publication or for PC
} on-screen image analysis, rather than printing to A4/A3. A Epson 4990 Photo
} 4,800 dpi scan of Kodak 4489 negative is around 250 Mb in TIF format, at
} 2,400 dpi it drops to a 60Mb TIF file with little different in image
} quality. There no reason however not to go for the better 6,400 dpi Epson
} V750 Pro, even if you scan mainly at 1,200 dpi, as it's only a bit more
} money (and not ours). The 6,400 dpi will be useful for enlargement of
} selected areas (scanning at 3,200 dpi being optimal).
}
} Perhaps one downside to the V750 Pro is that it works best with the
} slide/film holders and their little leg supports. Some sizes of TEM film may
} have small parts of the image hidden by a 4x5" film holder. You can source
} third party film holders though (see Doug Fisher), or you can just drop them
} onto the platen and live with a possible small drop in resolution. As
} mentioned you can get interference patterns (swirls) if the negative is
} placed on the platen rather than using the 4x5" film holder. This is
} probably caused by a slightly damp negative (high humidity) or the glass
} platen having greasy finger marks. So far I have always got rid of this by
} cleaning the platen (50% propanol/50% water with soft tissue and air-bulb
} blow dry - also great for finger smudged VDU screens). Remove film from the
} platen with a sheet of card rather than fingers (i.e. never touch the glass
} platen). No-one here ever bothers to use the Epson 4990's 4x5" film holders
} as it obscures part of the negative, only takes a few films and is far more
} fiddly. They just place six TEM negatives directly on the platen (correct
} side up).
}
} If you are really really serious about scanning film for some reason there
} is also the likes of professional flatbed scanners such as the Kodak
} ‘Creo’£15k [10,000 dpi] IQSmart 3, the £30k [8000 to 14000 dpi] EverSmart
} Supreme II flatbeds (www.kodak.com). However cheaper consumer ‘photo’ flat
} beds such as the new 6,400 dpi Epson V750 and V750 Pro come in at £500 and
} £650 respectively, and I can't see any reason to spend more for infrequent
} scans of large format B&W film, as you will rarely, if ever, scan at maximum
} resolution. They also have convenient USB2 and Firewire interfaces and work
} with Apples or PCs.
}
} You will have to spend a bit of time working on the best twain scan settings
} and images will probably need some post-editing in Photoshop CS3 to get
} optimal scanned image quality.
}
} But the choice is yours. Do however have a look at
} http://www.photo-i.co.uk for Independent reviews of some prosumer large
} format (A4) film scanners (not the i900). Also note that these cheaper
} scanners are for light use, if you want to scan hundreds of films a day, and
} not be chained to the scanner, look elsewhere and with a deeper pocket.
}
} Regards
}
} Keith
}
} PS. My 'Scanning film on a budget' Microscopy Today article has been updated
} and reprinted in Infocus (March 2007) the UK Royal Microscopical society's
} magazine. I can't send a pdf though as the editor hasn't passed on a
} corrected version yet. I can only send a scan of the article taken using my
} home 4,800 dpi Canon 9950F (scanned at 600 dpi) - but don't try that at home
} with your £2,000 Nikon Coolscan 9000.
}
} PPS. As mentioned the now withdrawn Canon 9550F has a terrible twain
} software interface(Scangear), the Epsons Scan one is miles better, so I
} would avoid the Canon even if you can still find it [unless its only ever
} being used for scanning photographs or with standard film holder sizes].
} Interestingly Canon scrapped their dedicated 35mm film scanners for the
} 9950F (and they should know something about film photography) but the poor
} Scangear twain interface didn't make many friends. I bought the 9950F just
} before the Epson 4990 Photo came in - which I later purchased for work use,
} mainly for TEM negatives, 2D gel film and reflective scans.
}
}
} ---------------------------
} Dr Keith J Morris
} Imaging Facilities Manager
} Cell Biology
} Institute of Ophthalmology
} UCL, London EC1V 9EL
}
}
}
}
}
} -----Original Message-----
} X-from: jgross-at-neuron.uchc.edu [mailto:jgross-at-neuron.uchc.edu]
} Sent: 26 April 2007 19:55
} To: keith.morris-at-ucl.ac.uk
} Subject: [Microscopy] Scanners for TEM negatives
}
}
}
}
} ----------------------------------------------------------------------------
} The Microscopy ListServer -- CoSponsor: The Microscopy Society of America
} To Subscribe/Unsubscribe -- http://www.microscopy.com/MicroscopyListserver
} On-Line Help http://www.microscopy.com/MicroscopyListserver/FAQ.html
} ----------------------------------------------------------------------------
}
} Our lab needs to purchase a new scanner for our TEM negatives. We
} have narrowed our choices to either the Epson Perfection V750
} (recommended by Keith Young in the May 2006 issue of Microscopy
} Today) or the Microtek ScanMaker i900. The major difference between
} the two seems to be the "glassless" scanning feature of the Microtek.
} Has anyone had first-hand experience of the film scanning ability of
} either one of these scanners? Or are there any quirks that would
} make one of them less desirable?
}
} Thank you,
} Julie Gross
} Kent Morest Lab
} Dept. of Neuroscience
} UCONN Health Center
} Farmington, CT 06030
} jgross-at-neuron.uchc.edu
}
}
}
}
} ==============================Original Headers==============================
} 32, 24 -- From keith.morris-at-ucl.ac.uk Fri Apr 27 07:11:58 2007
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} 32, 24 -- Subject: RE: [Microscopy] Scanners for TEM negatives
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From: john_mackenzie-at-ncsu.edu
Date: Fri, 27 Apr 2007 23:38:17 -0500
Subject: [Microscopy] Re: Scanners for TEM Negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Folks:

I've been away from my desk and missed this thread. I don't like to jump
in at the end but I don't agree that the Microtek is the way to go. The
two problems that I have with the Microtek have been speed and
resolution. Although they may have inproved the resolution some the
speed issue sounds about the same. The glassless idea is ok but the only
reason that you might be worried about the resolution is if you are
working in the 2000 ppi range. We do do our work prints at 1200 dpi but
high res scanns are at 4800. I have actually measured the resolution in
transparency mode at a true 2000 pixels per inch with the 4870 and 4990
Epsons. The Epson D750 Pro is actuall better but has not been thru
testing as yet. (It sits on my desk next to the 4990) The big difference
is that the Epsons are 5 to 10 times faster at scanning. I was a
Microtek fan but nothing has come close to the Epsons in about 5 years.

I don't have alot of time but would like to put forth a few critically
important facts that we have* measured.*

1. The Silverfast driver is worthless.(The upgrade is worse than the
free teaser one) It is fast and inaccurate not good features for
scientific imaging. We use the slower and accurate twain driver that
comes with the Epson.for free
2. Always scan negatives as positive transparencies. If you don't think
this is true...Do it. The scanning range for scanning negatives is
smaller than the scanning range in the positive transparency mode.
3. We have been working on holders that fully support 4 negatives.
4. We normally have a 4990 or 4870 on each computer so that scanning can
be done while we do other things The D750 for --|8k x 8k
5. We insure that all "automatic" adjustments are turned off by hitting
reset before every scan.
6. We insure that all filters and all histograms are truly set to zero
and/or max/min This is an insidious problem. The manufacturers are
turning on filters and not resetting to zero or to max in the defaults.
Don't ask me why cause I don't know. They change this with every version
of the drivers so you must constantly check.

If you want really high resolution then the D750 has a liquid immersion
system that allows you to get higher than anything but the drum scanners.

Using the Epson we can prove that we get 8k by 8 k in 16 bit mode we see
--|3.7 O.D.The negative has 16k by 16k at 12 bits The D750 with immersion
might get us really close to this.(Remember the 4990 is only $450)

I will point out to those of you who may think that you don't need to
calibrate your scanners that I found one of mine was getting less than
half the resolution on one axis and was even worse on the other axis.An
astigmatic scanner I currently have about $3,500 in test targets that
I've been using to check. The very high end testing by MTF (modulation
transfer function on slanted lines) requires a unique system that is
currently not commercially available.

If people on the list are interested I'll try to flesh out some of this
stuff soon

John

John M. Mackenzie, Jr., PhD

Professor of Microbiology
Coordinator, Center for Electron Microscopy
North Carolina State University
Phone (919) 515-2664 Fax (919) 515-8293

--
John M. Mackenzie, Jr., PhD
Professor of Microbiology
Coordinator, Center for Electron Microscopy
North Carolina State University
Phone (919) 515-2664 Fax (919) 515-8293



==============================Original Headers==============================
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From: gary-at-gaugler.com
Date: Sat, 28 Apr 2007 00:17:39 -0500
Subject: [Microscopy] Scanners for TEM Negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Good selections. Don't get a UMAX scanner. I have
UMAX III SCSI and it has failed too many times.
Factory returns garner marginal improvements.

I think that any unit other than UMAX could be
a good solution. Caveat emptor.

gary g.


At 08:40 PM 4/27/2007, you wrote:
} ----------------------------------------------------------------------------
} The Microscopy ListServer -- CoSponsor: The Microscopy Society of America


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From: keith.morris-at-ucl.ac.uk
Date: Sat, 28 Apr 2007 06:42:39 -0500
Subject: [Microscopy] Re: Scanners for TEM Negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Just to clarify the email below:

My name should appear above the second message starting "Don't drop the humidity too low...." and not above the first message.

Ted

----- Original Message ----
X-from: Purdy Samuel Purdy {smpurdy-at-sbcglobal.net}
To: drteddunne-at-yahoo.com
Sent: Wednesday, April 25, 2007 4:31:31 AM

Hi John,

I haven't tried the Microtek i900, but your views echo my suspicions (that
the Epson V750 Pro is probably a faster and better scanner).

I can't easily post my scans of TEM negatives using a £8,000 Hasselblad
Flextight 484 and the lowly £250 Epson 4990 Photo as they come in at over
10Mb even with high jpeg compression (and my Hasselblad Flextight 484 TEM
film scans CD is in the attic somewhere).

In fact for my old 35mm 100ASA Agfa colour slide film (~120 lines per mm)
scan quality is virtually identical for both, with the Flextight giving
miniscule extra detail and less noise with very dark shadows. The film grain
is certainly resolved more clearly with the Flextight - it looks in-focus
more and less fuzzy, but this doesn't actually provide much more image
detail. This is probably because both scanners are resolving detail beyond
that of the film. The Epson 4990 image needed some Photoshop post-editing
though - ultra-sharp mask (sharpen), and shadow/highlight to resolve details
in dark shadow being the main ones. If a film scan looks bad, say too dark
or light, it normally means you have to adjust the scanners twain settings,
which can be laborious and often needs to be done for each slide.

However I have to say that with TEM Kodak 4489 (probably better than 200
lpm) there is more detail in some areas of the image with the Flextight 484
scan. In other areas there is not a jot of difference. This could be a
focussing problem with the 4990 Photo, or vibration, and/or the fact that I
didn't use the 4x5" film holders, and just put the film on the glass platen
(as that’s what we tend to do to allow 6 fast negative scans per go).
However whether this slight extra detail is really required, given the 30
times higher price of the Hasselblad, is largely dependent to the users
requirements, it would probably be lost at 1,200 dpi scanning. Plus, the
Hasselblad has a yearly maintenance contract of around £800, and the cheap
upmarket sibling 6,400 dpi Epson V750 Pro (£550) is even better than the
4,800 dpi 4990 Photo I use.

However given the price of a digital camera on a TEM, £8,000 for a top
quality Hasselblad scanner isn't ludicrous (but you can't do A4 reflective
scans so you still need that standard A4 flatbed). See your local
reprographics department if you want a tour of a Flextight (but don't expect
the operators to always know too much about it technically - they probably
won't spend an hour or two getting the perfect scan from a crucial
negative). See http://www.hasselblad.com/products/scanners.aspx for
Hasselblads latest scanners (X1 - £7,500 and X5 - £12,000). The prices &
some details are also at
http://www.robertwhite.co.uk/hasselblad.htm#LabelHFS.

Always remember that the best scanner in the world will always degrade the
image compared to original film, as going through a series of optics again
will lose some ultra-fine detail - just as the original film lost detail via
limitations of the camera optics/film when the image was captured. The
amount of degradation is dependent on scanner optics and mechanism quality
(and thus generally price, although there are no doubt expensive lemons and
cheap stars out there). Thus although a digital and professional slide film
SLR camera will capture similar image detail from a scene, the image from
the film will always suffer when scanned into digital form. You can see this
extra detail in the original film, compared to the scanned image, by simply
looking at the film with an 8x magnifier over a light-box (it's not
startling, but it is definitely there, and it's seen easiest with colour
slide film of say writing on the side of ship, a house or our kids faces).

Rather like taking a picture with a quality compact digital camera it can
look great, but compare it with the same view taken with a digital SLR and
the difference in detail at high magnification can be quite startling. Your
scanner may be producing good images at 1,200 dpi, but it might not match
the best at maximum resolution or at that downscaled to 1,200 dpi using a
quality canner.

Personally I don't actually mind Silverfast, but it's not a very easy
interface. I use $120 Silverfast Ai with my Canon 9950F, as Canon's Scangear
twain software is so very poor it simply makes Silverfast look good
(Silverfast doesn't have Fare dust removal support though, as Canon won't
tell them how it works, you only get support for Digital ICE on Epson and
other scanners).

Regards

Keith

---------------------------
Dr Keith J Morris
Imaging Facilities Manager
Cell Biology
Institute of Ophthalmology
UCL, London EC1V 9EL





-----Original Message-----
X-from: john_mackenzie-at-ncsu.edu [mailto:john_mackenzie-at-ncsu.edu]
Sent: 28 April 2007 05:43
To: keith.morris-at-ucl.ac.uk

Folks:

I've been away from my desk and missed this thread. I don't like to jump
in at the end but I don't agree that the Microtek is the way to go. The
two problems that I have with the Microtek have been speed and
resolution. Although they may have inproved the resolution some the
speed issue sounds about the same. The glassless idea is ok but the only
reason that you might be worried about the resolution is if you are
working in the 2000 ppi range. We do do our work prints at 1200 dpi but
high res scanns are at 4800. I have actually measured the resolution in
transparency mode at a true 2000 pixels per inch with the 4870 and 4990
Epsons. The Epson D750 Pro is actuall better but has not been thru
testing as yet. (It sits on my desk next to the 4990) The big difference
is that the Epsons are 5 to 10 times faster at scanning. I was a
Microtek fan but nothing has come close to the Epsons in about 5 years.

I don't have alot of time but would like to put forth a few critically
important facts that we have* measured.*

1. The Silverfast driver is worthless.(The upgrade is worse than the
free teaser one) It is fast and inaccurate not good features for
scientific imaging. We use the slower and accurate twain driver that
comes with the Epson.for free
2. Always scan negatives as positive transparencies. If you don't think
this is true...Do it. The scanning range for scanning negatives is
smaller than the scanning range in the positive transparency mode.
3. We have been working on holders that fully support 4 negatives.
4. We normally have a 4990 or 4870 on each computer so that scanning can
be done while we do other things The D750 for --|8k x 8k
5. We insure that all "automatic" adjustments are turned off by hitting
reset before every scan.
6. We insure that all filters and all histograms are truly set to zero
and/or max/min This is an insidious problem. The manufacturers are
turning on filters and not resetting to zero or to max in the defaults.
Don't ask me why cause I don't know. They change this with every version
of the drivers so you must constantly check.

If you want really high resolution then the D750 has a liquid immersion
system that allows you to get higher than anything but the drum scanners.

Using the Epson we can prove that we get 8k by 8 k in 16 bit mode we see
--|3.7 O.D.The negative has 16k by 16k at 12 bits The D750 with immersion
might get us really close to this.(Remember the 4990 is only $450)

I will point out to those of you who may think that you don't need to
calibrate your scanners that I found one of mine was getting less than
half the resolution on one axis and was even worse on the other axis.An
astigmatic scanner I currently have about $3,500 in test targets that
I've been using to check. The very high end testing by MTF (modulation
transfer function on slanted lines) requires a unique system that is
currently not commercially available.

If people on the list are interested I'll try to flesh out some of this
stuff soon

John

John M. Mackenzie, Jr., PhD

Professor of Microbiology
Coordinator, Center for Electron Microscopy
North Carolina State University
Phone (919) 515-2664 Fax (919) 515-8293

--
John M. Mackenzie, Jr., PhD
Professor of Microbiology
Coordinator, Center for Electron Microscopy
North Carolina State University
Phone (919) 515-2664 Fax (919) 515-8293



==============================Original Headers==============================
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==============================Original Headers==============================
38, 24 -- From keith.morris-at-ucl.ac.uk Sat Apr 28 06:42:39 2007
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From: PRICE-at-gw.med.sc.edu
Date: Sat, 28 Apr 2007 08:26:01 -0500
Subject: [Microscopy] viaWWW: Confocal Workshop June 18-21

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This Question/Comment was submitted to the Microscopy Listserver
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Email: {PRICE-at-gw.med.sc.edu}
Name: "Bob Price"

Organization: University of South Carolina

Title-Subject: [Filtered] Confocal Workshop

Question:
The University of South Carolina Instrumentation Resource Facility and the South Carolina EPSCoR (NSF) and INBRE (NIH) programs will be hosting a hands on workshop in Basic Confocal Microscopy from June 18-21. Full details concerning the workshop and registration information can be found at http://www.scepscor.org/outreach/workshops/confocal-microscopy/home.html

The workshop will consist of both lectures and laboratory sessions and is directed towards beginning and intermediate level users of confocal microscopy. Topics covered will include the basics of fluorescence and selection of probes, specimen fixation and staining, proper set up of operating parameters for collection of images, composition of digital confocal images, the use of image enhancement and analysis programs such as Photoshop and Metamorph for confocal images, and the use of 3-D reconstruction programs such as AMIRA.

Instructors for the workshop will include Dr. Jay Jerome from Vanderbilt University, Dr. John Mackenzie from North Carolina State University, Dr. Tom Trusk from the Medical University of South Carolina, and Drs. Bob Price and John Fuseler from the USC School of Medicine.

A variety of confocal microscopes including the BD CARV spinning disk, Leica, Nikon, Olympus, and Zeiss systems are scheduled to be on hand for the laboratory sessions. Applications experts from each of the companies will also be on hand for discussion of their specific systems. Participants are encouraged to bring their own specimens for sample preparation and imaging sessions, but a variety of cell culture and tissue sections will also be available for laboratory sessions on fluorescent staining and imaging.

For further information or questions please contact Bob Price (Price-at-med.sc.edu)

Workshop on Basic Confocal Microscopy
Monday June 18, 2007
8:30-9:00 Registration and Continental Breakfast, Bldg 1, Room B59 USC School of Medicine
9:00-9:15 Welcome and Logistics
9:15-10:15 Introduction and Overview of Confocal Microscopy: Jay Jerome (Vanderbilt University) and Bob Price (USC School of Medicine)
10:15-10:45 Break and Discussion
10:45-12:00 Basics of Fluorescence, Dye Characteristics: Jerome and Price
12:00-1:00 Lunch (Provided) and discussion
1:00-3:00 Specimen Preparation: Jerome and Price
3:00-3:30 Break and Discussion
3:30-?? Lab * Specimen Preparation and processing: Processing of own samples or samples will be provided. Fixation through overnight primary antibody incubation
Dinner on your own

Tuesday June 19, 2007
8:30-9:00 Continental Breakfast * Room B59
9:00-10:00 Lab - Wash specimens and secondary antibody incubation
10:00-10:30 Break and Discussion
10:30-12:00 Components, proper set up of operating parameters, and types of confocal microscopes: Jerome and Price
12:00-1:30 Lunch (Provided) and Specimen Processing
1:30-2:30 Digital Images in Confocal Microscopy * Jerome and Price
2:30-4:00 Lab * finish specimen processing
4:00-6:00 Time on Instruments (BD CARV, Leica, Nikon, Olympus, Zeiss systems are scheduled to be available)
Dinner on your own

Wednesday June 20, 2007
8:30-9:00 Continental Breakfast * Room B59
9:00-12:00 Photoshop, etc with confocal images (John Mackenzie * North Carolina State University)
12:00-1:00 Lunch
1:00-5:00 Time on Confocal Instruments and Software
6:00-?? Reception on Lake Murray

Thursday June 21, 2007
8:30-9:00 Continental Breakfast * Room B59
9:00-11:00 3-D reconstruction of confocal data sets with AMIRA (Tom Trusk * Medical University of South Carolina)
11:00-12:00 Ethics in Use of Confocal Images, Available Resources, Discussion
12:00 - 4:00 Lunch and additional time on Confocal Instruments and Software (Photoshop, AMIRA, Metamorph)


Robert L. Price, PhD
Research Professor and
Director, Instrumentation Resource Facility
School of Medicine, USC
Bldg 1 Room B60
6439 Garner's Ferry Road
Columbia, SC 29208

Fax: 803-733-1533
Telephone: 803-733-3392



---------------------------------------------------------------------------

==============================Original Headers==============================
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From: john_mackenzie-at-ncsu.edu
Date: Sat, 28 Apr 2007 12:32:16 -0500
Subject: [Microscopy] Scanners for TEM Negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Gary:

It is in fact quite important to insure that the negatives are held at a
uniform 1mm distance. This is why we went to trouble to machine special
holders. It is odd to make a $150 holder for a $450 scanner but 3.25 by
4.00 is an odd size. It was particularly upsetting as the first
prototypes didn't work and would only scan the center area. You can buy
extra 4 x 5 holders for $5.00 but you have to watch that the free edge
is not bent.

John

John M. Mackenzie, Jr., PhD
Professor of Microbiology
Coordinator, Center for Electron Microscopy
North Carolina State University
Phone (919) 515-2664 Fax (919) 515-8293



Gary Gaugler wrote:
} Good selections. Don't get a UMAX scanner. I have
} UMAX III SCSI and it has failed too many times.
} Factory returns garner marginal improvements.
}
} I think that any unit other than UMAX could be
} a good solution. Caveat emptor.
}
} gary g.
}
}
} At 08:40 PM 4/27/2007, you wrote:
} } ----------------------------------------------------------------------------
} }
} } The Microscopy ListServer -- CoSponsor: The Microscopy Society of
} } America
} } To Subscribe/Unsubscribe --
} } http://www.microscopy.com/MicroscopyListserver
} } On-Line Help http://www.microscopy.com/MicroscopyListserver/FAQ.html
} } ----------------------------------------------------------------------------
} }
} }
} } Folks:
} }
} } I've been away from my desk and missed this thread. I don't like to jump
} } in at the end but I don't agree that the Microtek is the way to go. The
} } two problems that I have with the Microtek have been speed and
} } resolution. Although they may have inproved the resolution some the
} } speed issue sounds about the same. The glassless idea is ok but the only
} } reason that you might be worried about the resolution is if you are
} } working in the 2000 ppi range. We do do our work prints at 1200 dpi but
} } high res scanns are at 4800. I have actually measured the resolution in
} } transparency mode at a true 2000 pixels per inch with the 4870 and 4990
} } Epsons. The Epson D750 Pro is actuall better but has not been thru
} } testing as yet. (It sits on my desk next to the 4990) The big difference
} } is that the Epsons are 5 to 10 times faster at scanning. I was a
} } Microtek fan but nothing has come close to the Epsons in about 5 years.
} }
} } I don't have alot of time but would like to put forth a few critically
} } important facts that we have* measured.*
} }
} } 1. The Silverfast driver is worthless.(The upgrade is worse than the
} } free teaser one) It is fast and inaccurate not good features for
} } scientific imaging. We use the slower and accurate twain driver that
} } comes with the Epson.for free
} } 2. Always scan negatives as positive transparencies. If you don't think
} } this is true...Do it. The scanning range for scanning negatives is
} } smaller than the scanning range in the positive transparency mode.
} } 3. We have been working on holders that fully support 4 negatives.
} } 4. We normally have a 4990 or 4870 on each computer so that scanning can
} } be done while we do other things The D750 for --|8k x 8k
} } 5. We insure that all "automatic" adjustments are turned off by hitting
} } reset before every scan.
} } 6. We insure that all filters and all histograms are truly set to zero
} } and/or max/min This is an insidious problem. The manufacturers are
} } turning on filters and not resetting to zero or to max in the defaults.
} } Don't ask me why cause I don't know. They change this with every version
} } of the drivers so you must constantly check.
} }
} } If you want really high resolution then the D750 has a liquid immersion
} } system that allows you to get higher than anything but the drum
} } scanners.
} }
} } Using the Epson we can prove that we get 8k by 8 k in 16 bit mode we see
} } --|3.7 O.D.The negative has 16k by 16k at 12 bits The D750 with
} } immersion
} } might get us really close to this.(Remember the 4990 is only $450)
} }
} } I will point out to those of you who may think that you don't need to
} } calibrate your scanners that I found one of mine was getting less than
} } half the resolution on one axis and was even worse on the other axis.An
} } astigmatic scanner I currently have about $3,500 in test targets that
} } I've been using to check. The very high end testing by MTF (modulation
} } transfer function on slanted lines) requires a unique system that is
} } currently not commercially available.
} }
} } If people on the list are interested I'll try to flesh out some of this
} } stuff soon
} }
} } John
} }
} } John M. Mackenzie, Jr., PhD
} }
} } Professor of Microbiology
} } Coordinator, Center for Electron Microscopy
} } North Carolina State University
} } Phone (919) 515-2664 Fax (919) 515-8293
} }
} } --
} } John M. Mackenzie, Jr., PhD
} } Professor of Microbiology
} } Coordinator, Center for Electron Microscopy
} } North Carolina State University
} } Phone (919) 515-2664 Fax (919) 515-8293
} }
} }
} }
} } ==============================Original
} } Headers==============================
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From: williamchai1979-at-gmail.com
Date: Sat, 28 Apr 2007 20:39:27 -0500
Subject: [Microscopy] SEM-EDS for suspended particulate in water column

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Dear all,
I am wonder anyone have been using the SEM-EDS to study the characteristic
of suspended particulate(0.45um filter paper retained suspended particulate)
in water column relate to suspended particulate trace metals or any
reference on this topic, cause mostly i get from journal is airborne
particle. i already have a set of data on EDS of my sample and SEM image on
my sample as well. I am having a hard time to find the journal report the
suspended particulate in water column. It will be great to heard respond
from u all. Thanks for your valuable time.

Have a nice day.


regard
William Wong

==============================Original Headers==============================
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From: keith.morris-at-ucl.ac.uk
Date: Sun, 29 Apr 2007 08:53:41 -0500
Subject: [Microscopy] Scanners for TEM Negatives

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

I agree it is important to use the holders for important scans at high
resolution (greater than 800 dpi), although these modern flatbed film
scanners do have a pretty good depth of field for low resolution scans - you
can happily scan toys, leaves, seeds etc..).

Everyone here shuns the film holders as they tend to do 800 dpi scans only
(rarely even 1200 dpi). I mention the holders to all our users but they
always decline on the grounds that the images look fine for their purpose
(thus they basically can't be bothered - even after spending weeks getting
the samples to the TEM negative stage). However invariably in such cases
they generally only require a very small photo for a publication or talk,
the magnification being done quite rightly at the TEM rather than when
scanning the film. I only invariably use the film holders when scanning TEM
negatives above 800 dpi (and that's only been for the odd scanning film
article I have written) - my interest is almost exclusively the scanning of
35mm colour slide film, that come in their own little holders, or 35mm
colour negatives that have to be fitted into the 35mm film strip holder
unless you want a really bad time in Photoshop.

Those interested in things like counting gold particles or measuring
distances with TEM images via MetaMorph can occasionally be coerced into
using the 4x5" holders. As I run the confocal/time-lapse/laser dissection
light microscopy side of things at the institute, the scanner we use is
provided for the TEM users merely as an occasional service for old film.
Apple fans here still stick to our old Agfa [Microtek] 2550T scanner with
it's glass sandwich system, as it's attached to an cuddly Apple (plus they
paid the £5,000 for it back in 2000).

Their TEM microscope has now been converted to a rather expensive Gatan
digital camera system and wet EM film processing has largely ceased. I have
to say that the TEM film doesn't flatten completely in the Epson 4x5"
holders, the film being only held on three sides. Plus they can only hold
two smaller Kodak negatives at a time and obscure bits of the image. I would
think that our workshop would easily be able to make a better version to
hold more negatives fairly easily, but the requirement for scanning TEM film
is now on the wane here. My main concern would be the long term archiving
and storage of these very large digital images, as modern TEM film was such
a stable medium in comparison, but that isn't really my problem.

Regards

Keith

-----Original Message-----
X-from: john_mackenzie-at-ncsu.edu [mailto:john_mackenzie-at-ncsu.edu]
Sent: 28 April 2007 18:40
To: keith.morris-at-ucl.ac.uk

Gary:

It is in fact quite important to insure that the negatives are held at a
uniform 1mm distance. This is why we went to trouble to machine special
holders. It is odd to make a $150 holder for a $450 scanner but 3.25 by
4.00 is an odd size. It was particularly upsetting as the first
prototypes didn't work and would only scan the center area. You can buy
extra 4 x 5 holders for $5.00 but you have to watch that the free edge
is not bent.

John

John M. Mackenzie, Jr., PhD
Professor of Microbiology
Coordinator, Center for Electron Microscopy
North Carolina State University
Phone (919) 515-2664 Fax (919) 515-8293




==============================Original Headers==============================
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From: Colin.Veitch-at-csiro.au
Date: Mon, 30 Apr 2007 00:29:42 -0500
Subject: [Microscopy] Video out from a Hitachi S4300SE/N

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

G'day,

We have just acquired a Hitachi S4300 SE/N and I was wondering if anyone
had captured the video signal from one of these SEM's. If so, what
method was used and found to be effective - capture to tape and then
conversion to digital or direct capture to PC via a frame grabber.

Any ideas, pit-falls, card types etc would be much appreciated. I
believe the output is NTSC.

Cheers and thank you.

Colin Veitch

Electron Microscopist
CSIRO Textile and Fibre Technology
PO Box 21, BELMONT, Vic. 3216. Australia.
colin.veitch-at-csiro.au
http://www.tft.csiro.au
+61 (0) 3 5246 4000
0438 538 475
+61 (0) 3 5246 4811

The information contained in this e-mail message may be privileged or
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received this message in error, please telephone CSIRO Textile and Fibre
Technology on +61 3 5246 4000.



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From: charlesping-at-hotmail.com
Date: Mon, 30 Apr 2007 08:24:27 -0500
Subject: [Microscopy] viaWWW: pins definition for Varian gun unit

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Email: charlesping-at-hotmail.com
Name: Charles

Organization: University of York

Title-Subject: [Filtered] The pins definition for Varian gun unit

Question: Dear all

I am going to use the Varian electron gun control unit 981-2745 and scanning sample positioner 981-2757A to control the electron gun we built. In the manual we didn't find any information for the pin definition for the cable connecting the gun control unit with the electron gun , either the gun scanning unit with the electron gun. Did anyone use this two units before? Could you tell me the pins definition of these two units' connectors to the gun?
Many thanks

Charles
Department of Electronics
University of York
UK

---------------------------------------------------------------------------

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From: ph2-at-sprynet.com
Date: Mon, 30 Apr 2007 09:39:59 -0500
Subject: [Microscopy] SEM-EDS for suspended particulate in water column

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Can you be more specific?

Drinking water
Waste water
Surface runoff
Inland Surface water bodies
Ocean water bodies

Tony

......................................................................
Andrew Anthony "Tony" Havics, CHMM, CIH, PE
pH2, LLC
5250 E US 36, Suite 830
Avon, IN 46123
(317) 718-7020 off
(317) 718-7038 fax
(317) 409-3238 cell

90% of Risk Management is knowing where to place the decimal point...any
consultant can give you the other 10%(SM)

This message is from pH2. This message and any attachments may contain
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-----Original Message-----
X-from: williamchai1979-at-gmail.com [mailto:williamchai1979-at-gmail.com]
Sent: Saturday, April 28, 2007 9:46 PM
To: ph2-at-sprynet.com

Dear all,
I am wonder anyone have been using the SEM-EDS to study the characteristic
of suspended particulate(0.45um filter paper retained suspended particulate)
in water column relate to suspended particulate trace metals or any
reference on this topic, cause mostly i get from journal is airborne
particle. i already have a set of data on EDS of my sample and SEM image on
my sample as well. I am having a hard time to find the journal report the
suspended particulate in water column. It will be great to heard respond
from u all. Thanks for your valuable time.

Have a nice day.


regard
William Wong

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From: frah0010-at-umn.edu
Date: Mon, 30 Apr 2007 15:54:26 -0500
Subject: [Microscopy] auto particle ident

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Fellow microscopists,

I know that this topic arises at lease once a year, but software
advances so quickly nowadays that one- or two-year-old information is
often completely useless.

I'm seeking opinions and information on current methods for largely
automated particle classification based on color and shape/size in
images. I don't need an image acquisition system, and a gallery or
database feature just would be a bonus.

As I mentioned, I fear most of my information is outdated and comes
mostly from advertisements or product brochures. Before we were just
exploring what was out there, but now we have a real project for
using such software.

I know of a few options, like Soft Imaging System's analySIS
software, but its steep price tag to get all those bells and whistles
is likely going to be too high for the project.

I'd be interesting in hearing from colleagues about their experiences
(good and bad) with any programs in particular, and any sales people
can feel free to contact me with information as well.

Thanks all in advance,

Ellery

--------------------
Ellery E. Frahm
Research Fellow & Manager
Electron Microprobe Laboratory
University of Minnesota - Twin Cities
Department of Geology & Geophysics
Lab Website: http://probelab.geo.umn.edu
Personal Website: http://umn.edu/~frah0010

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From: bigelow-at-umich.edu
Date: Mon, 30 Apr 2007 16:36:18 -0500
Subject: [Microscopy] Diffusion Pmp cooling water

Contents Retrieved from Microscopy Listserver Archives
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} The question of providing cooling water for an oil diffusion pump is
} discussed in some detail in Sec. 5.8.1 (p. 215) of my book 'Vacuum
} Methods in Electron Microscopy' (available from SPI Supplies, M. E.
} Taylor, Ladd, etc). Basically, the primary requirement is to keep
} the temperature of the body of the diffusion pump at a temperature
} low enough to condense the vapor of the diffusion pump fluid as it
} strikes the wall of the pump . The pressure and
} flow rates are only secondary matters of concern as long as this
} requirement is met. I suggest you check the temperature of the
} cooling coils at the top of the pump, and of the water coming out of
} the water line. The water should be entering the pump at the top of
} the cooling coils and exiting from the bottom, so that the top of
} the pump wall is coolest. If the temperature there is "cool to the
} touch" it is probably all right, because most modern diffusion pump
} oils have rather low vapor pressures and readily condense at
} moderately cool temperatures - liquid nitrogen is not needed. The
} water flowing out of the bottom of the pump may be slightly warm to
} the touch, and the pump can still function properly.
}
} I do not recommend using water-glycol mixtures, for reasons given in
} my book. Instead I think it is better to use just distilled water,
} adding a bit of algaecide to prevent algae from growing in the
system. We used the algaecide Chloramine-T (the sodium salt of
N-chloro-p-toluenesulphonamide, available from specialty chemical
companies such as Alfa-Aldrich, Sigma, etc) at the level of 1 gram
per gallon for years with very satisfactory results. Algaecides are
also available from water bed and swimming pool suppliers. Using
} tubes and hoses in the circulating system that are
} completely opaque to light, and covering the reservoir to exclude
light, will also effectively limit growth of algae in the system. You should,
of course, have a good filter on the inlet to the supply line to catch any
} algae (or other debris) that does happen to get into the system.
--
--
Wilbur C. Bigelow, Professor Emeritus
Materials Sci. & Engr., Univ. of Michigan
Ann Arbor, Michigan 48109-2136
e-mail: bigelow-at-umich.edu;
Fx:734-763-4788; Ph:734-975-0858
Address mail to: 2911 Whittier Court
Ann Arbor, MI 48104-6731

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From: TindallR-at-missouri.edu
Date: Mon, 30 Apr 2007 17:02:38 -0500
Subject: [Microscopy] Labware washers

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

Dear Listers,

Does anyone have a recommendation for a laboratory glassware washer that
will fit under a counter (about like a home dishwasher size), handle
light duty of two or three loads a week, wash labware to a level
acceptable for EM use, and, ahem, not break the bank? Does something
like this exist for $5000 or thereabouts? Am I delusional? (Don't
answer that......)

We currently have users privileges on a really nice huge heavy duty lab
dishwasher, but the day is coming when this will end. Also, we don't
always have access exactly when we most need it. We want our own!

Thanks in advance. Vendor replies are most welcome.

Cheers,
Randy

Randy Tindall
Senior EM Specialist
Electron Microscopy Core Facility---We Do Small Well!
W125 Veterinary Medicine
University of Missouri
Columbia, MO 65211
Tel: (573) 882-8304
Fax: (573) 884-2227
Email: tindallr-at-missouri.edu
Web: http://www.emc.missouri.edu
On-line calendar:
http://biotech.rnet.missouri.edu/cgi-bin/Calcium310.pl?Op=Splash&Amount=
Week&NavType=Both&Type=TimePlan


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From: donovan-at-uoregon.edu
Date: Mon, 30 Apr 2007 17:04:01 -0500
Subject: [Microscopy] Re: Diffusion Pmp cooling water

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html

All,
For what it's worth, here's my two cents. I have found, after many
years of experimenting with all sorts of solutions and chemicals,
that the best coolant is pure distilled water.

But what about algae one might ask. Here's the secret: simply make
sure to replace all lines with black (opaque) rubber hoses and that
all sight glasses, flow meters and other light "windows" have a
removable cover of some sorts.

If you remove all sources of light, that green scummy algae will
never grow in your system! On the other hand when even a little light
is present, I've had algae grow in pure ethylene glycol! The stuff
mutates effortlessly it seems.

I've run half a dozen instruments this way for over ten years and
never seen any algae buildup (maybe just a few tiny rust flakes here
and there at the bottom of the chiller reservoir).


John J. Donovan donovan-at-uoregon.edu
University of Oregon (541) 346-4632 (office)
1260 Franklin Blvd (541) 346-4655 (probe)
Eugene, OR (541) 346-4778 (SEM)
97403-1272 (541) 346-4692 (FAX)

Lab Web: http://epmalab.uoregon.edu/
EPMA (SX100)Schedule: http://sweetwater.uoregon.edu/sx100
EPMA (SX50) Schedule: http://sweetwater.uoregon.edu/epma
SEM (Ultra) Schedule: http://sweetwater.uoregon.edu/zeiss
SEM (Quanta) Schedule: http://sweetwater.uoregon.edu/sem
Remote Access: http://epmalab.uoregon.edu/howto.htm
Personal: http://www.uoregon.edu/~donovan/



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From: emlabservices-at-cox.net
Date: Mon, 30 Apr 2007 18:04:29 -0500
Subject: [Microscopy] Re: Diffusion Pmp cooling water

Contents Retrieved from Microscopy Listserver Archives
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John,

Of all the various methods and opinions that arise relative to this subject,
I have to agree with you. Use distilled water, change it frequently, clean
the recirculating filter, for extended chiller life, and the instruments
won't be routinely stress-tested with overheating.

Bob Roberts
EM Lab Services, Inc.
449 NW 62nd St.
Topeka, Kansas 66617-1780
785.246.1232 voice
785.246.0168 fax
www.emlabservices.com



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From: sandra.filippi-at-montgomerycollege.edu
Date: Mon, 30 Apr 2007 20:15:12 -0500
Subject: [Microscopy] AskAMicroscopist: Building Criteria for Optical Microscope Lab

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Below is the result of your feedback form (NJZFM-ultra-55). It was submitted by (sandra.filippi-at-montgomerycollege.edu) from http://microscopy.com/Ask-A-Microscopist/Ask-A-Microscopist.html on Monday, April 30, 2007 at 20:12:50
---------------------------------------------------------------------------

Email: sandra.filippi-at-montgomerycollege.edu
Name: Sandra Lee Filippi, Campus Planner

Organization: montgomery college

Education: Graduate College

Location: Rockville MD

Question:


Dear Sir or Madam Microscopist:

Montgomery College is in design development for a new academic teaching science center. The lab planner for the design team is citing ASHRAE TC2.6 Guideline Criteria for use in Planning New Facilities and insists that we design to the VC-B level because the biology department uses compound microscopes with total magnification of 1,000x (oil immersion). I managed academic science labs for a two-year college for more than 20 years. We routinely used light microscopes at total magnification of 1,000x (oil immersion) in a facility built in 1965 without special vibration control. When we opened our new science center in 1995 it did not have special vibration control either. I have studied at Georgetown University and did student research at The NIH. Neither of these facilities required special vibration control for a light microscope.
I have consulted with the Westover Scientific Customer Service/Product Specialist ñ Microscopy who states, ìTo be honest with you I have never heard of such a thing, neither have my colleagues. ÝThere are tables that are manufactured to reduce vibrations, but Iíve never heard of a building being designed around a microscope. ÝWe have customers who use microscopes in old buildings all over the world. Westover recommends that a microscope be used on a vibration free surface which typically means not locating your microscope on a table with other equipment that can cause vibrations such as fans and other lab equipment. Microscopes have been used for years and years on standard benchtops and other tables without issue. It's not our position to recommend additional support when building a new structure. In my entire career I have never heard of this requirement.î Westover manufactures microscopes for Fisher Scientific.
The lab planner is going to cost us dearly unless I can refute his recommendation. What is your professional opinion in this matter? Thank you very much for your time.
Sandra

Sandra Lee Filippi, Campus Planner
Montgomery College
Suite 200
40 West Gude Drive Room 223
Rockville MD 20850-1166
301.251.7362 vox
301.251.7379 fax
240.882.6672 cell


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From: ph2-at-sprynet.com
Date: Mon, 30 Apr 2007 21:13:23 -0500
Subject: [Microscopy] AskAMicroscopist: Building Criteria for Optical

Contents Retrieved from Microscopy Listserver Archives
http://www.microscopylistserver.com/MicroscopyListserver/MicroscopyArchives.html


1. A recent study was published in Sound and Vibration on Microscope
Acceptability of vibration for optical ones. (I'm at home and don't have a
copy with me)

- Vibration Sensitivity of Laboratory Bench Microscopes
Hal Amick and Matthew Stead, Colin Gordon & Associates

Benchtop optical microscopes are among the most common tools found in R&D
facilities. The importance of vibration isolation to maximize image quality
is discussed. Vibration criteria are presented.

2. I talked to the author last week (I have always been interested in
this since 3D vibration analysis work at GA Tech years ago) about some other
things that could be used as criteria for assessment and asked him to submit
an abstract for the upcoming Inter-Micro in Chicago, IL in July. Hopefully
he'll make it. In the mean time if you need a copy of the article contact
me or the S&V journal (It's not on their website yet
http://www.sandv.com/home.htm ).

3. This article does not cover the building aspects, but a good
vibration engineer could help there in conjunction with a structural
engineer, particularly in combination with the frequency response data from
this article.

Tony

.....................................................................
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pH2, LLC
5250 E US 36, Suite 830
Avon, IN 46123
(317) 718-7020 off
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90% of Risk Management is knowing where to place the decimal point...any
consultant can give you the other 10%(SM)

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-----Original Message-----
X-from: sandra.filippi-at-montgomerycollege.edu
[mailto:sandra.filippi-at-montgomerycollege.edu]
Sent: Monday, April 30, 2007 9:21 PM
To: ph2-at-sprynet.com

Below is the result of your feedback form (NJZFM-ultra-55). It was
submitted by (sandra.filippi-at-montgomerycollege.edu) from
http://microscopy.com/Ask-A-Microscopist/Ask-A-Microscopist.html on Monday,
April 30, 2007 at 20:12:50
---------------------------------------------------------------------------

Email: sandra.filippi-at-montgomerycollege.edu
Name: Sandra Lee Filippi, Campus Planner

Organization: montgomery college

Education: Graduate College

Location: Rockville MD

Question:


Dear Sir or Madam Microscopist:

Montgomery College is in design development for a new academic teaching
science center. The lab planner for the design team is citing ASHRAE TC2.6
Guideline Criteria for use in Planning New Facilities and insists that we
design to the VC-B level because the biology department uses compound
microscopes with total magnification of 1,000x (oil immersion). I managed
academic science labs for a two-year college for more than 20 years. We
routinely used light microscopes at total magnification of 1,000x (oil
immersion) in a facility built in 1965 without special vibration control.
When we opened our new science center in 1995 it did not have special
vibration control either. I have studied at Georgetown University and did
student research at The NIH. Neither of these facilities required special
vibration control for a light microscope.
I have consulted with the Westover Scientific Customer Service/Product
Specialist ñ Microscopy who states, ìTo be honest with you I have never
heard of such a thing, neither have my colleagues. ÝThere are tables that
are manufactured to reduce vibrations, but Iíve never heard of a building
being designed around a microscope. ÝWe have customers who use microscopes
in old buildings all over the world. Westover recommends that a microscope
be used on a vibration free surface which typically means not locating your
microscope on a table with other equipment that can cause vibrations such as
fans and other lab equipment. Microscopes have been used for years and
years on standard benchtops and other tables without issue. It's not our
position to recommend additional support when building a new structure. In
my entire career I have never heard of this requirement.î Westover
manufactures microscopes for Fisher Scientific.
The lab planner is going to cost us dearly unless I can refute his
recommendation. What is your professional opinion in this matter? Thank
you very much for your time.
Sandra

Sandra Lee Filippi, Campus Planner
Montgomery College
Suite 200
40 West Gude Drive Room 223
Rockville MD 20850-1166
301.251.7362 vox
301.251.7379 fax
240.882.6672 cell


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