Leica slide scanner calibration

[Michael Giacomelli]

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I had some pathology slides scanned at a local imaging core on an
Aperio scanner, but the color appears to be quite off.  Using the
built in correction in the aperio visualization software (which I
believe uses the correction information from the scanner), my H&E
slides are kind of a hot, oversaturated pink.  Disabling it brings it
closer to reality, but its still much too saturated.  Just to convince
myself, I looked side by side between the scanned images and the
original slides and used a second monitor.  Something is wrong.

I don't think this is my monitor, its an 8 bit IPS panel thats been
color calibrated to ~100% sRGB using an X-Rite.  Besides giving
excellent accuracy in the X-Rite measurements, other images look fine.

My assumption is that it has to be the scanner itself.  Has anyone had
this problem before?  I'm going to go back to the imaging core and try
to talk to them about it, but I was hoping to find out a little bit
more about the problem so I don't sound clueless when I say that my
images look 'funny'.

Mike

[Armstrong, Brian]

Hello Mike, I believe that some scanners use a default gamma setting of 0.45 for BF imaging. If this is the case then with the gamma at 1.0 it will appear oversaturated. Take a look at your gamma settings on Aperio Image Scope and see where it is set. Try the gamma at 0.45 and see how it looks. Ask your imaging partner what the gamma setting is on the Aperio scanner.

Cheers,

Brian Armstrong PhD
Director, Light Microscopy Core
Beckman  Research Institute



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michael Giacomelli
Sent: Monday, April 06, 2015 4:02 PM
To: [hidden email]
Subject: Leica slide scanner calibration

*****
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*****

I had some pathology slides scanned at a local imaging core on an Aperio scanner, but the color appears to be quite off.  Using the built in correction in the aperio visualization software (which I believe uses the correction information from the scanner), my H&E slides are kind of a hot, oversaturated pink.  Disabling it brings it closer to reality, but its still much too saturated.  Just to convince myself, I looked side by side between the scanned images and the original slides and used a second monitor.  Something is wrong.

I don't think this is my monitor, its an 8 bit IPS panel thats been color calibrated to ~100% sRGB using an X-Rite.  Besides giving excellent accuracy in the X-Rite measurements, other images look fine.

My assumption is that it has to be the scanner itself.  Has anyone had this problem before?  I'm going to go back to the imaging core and try to talk to them about it, but I was hoping to find out a little bit more about the problem so I don't sound clueless when I say that my images look 'funny'.

Mike


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[mcammer]

The few times we have calibrated scanners we laid a series on ND filters down .  Used to do something similar back in the days of video cameras...
=========================================================================
 Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center
                          Cell:  914-309-3270     Temporary location:  SK2-7
          http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Armstrong, Brian
Sent: Monday, April 06, 2015 7:19 PM
To: [hidden email]
Subject: Re: Leica slide scanner calibration

Hello Mike, I believe that some scanners use a default gamma setting of 0.45 for BF imaging. If this is the case then with the gamma at 1.0 it will appear oversaturated. Take a look at your gamma settings on Aperio Image Scope and see where it is set. Try the gamma at 0.45 and see how it looks. Ask your imaging partner what the gamma setting is on the Aperio scanner.

Cheers,

Brian Armstrong PhD
Director, Light Microscopy Core
Beckman  Research Institute



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michael Giacomelli
Sent: Monday, April 06, 2015 4:02 PM
To: [hidden email]
Subject: Leica slide scanner calibration

*****
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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

I had some pathology slides scanned at a local imaging core on an Aperio scanner, but the color appears to be quite off.  Using the built in correction in the aperio visualization software (which I believe uses the correction information from the scanner), my H&E slides are kind of a hot, oversaturated pink.  Disabling it brings it closer to reality, but its still much too saturated.  Just to convince myself, I looked side by side between the scanned images and the original slides and used a second monitor.  Something is wrong.

I don't think this is my monitor, its an 8 bit IPS panel thats been color calibrated to ~100% sRGB using an X-Rite.  Besides giving excellent accuracy in the X-Rite measurements, other images look fine.

My assumption is that it has to be the scanner itself.  Has anyone had this problem before?  I'm going to go back to the imaging core and try to talk to them about it, but I was hoping to find out a little bit more about the problem so I don't sound clueless when I say that my images look 'funny'.

Mike


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[Michael Giacomelli]

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Hi Brian,

I'm a little surprised that this is an issue, but I think you may be
right.  Adjusting the gamma by approximately that amount makes the
images look better. I'm not certain they're correct, but its certainly
much better.

A question though:  why is this even a problem?  As I understand it,
the Aperio format includes color calibration information from the
scanner (theres an option to apply it in their software), and it will
take the color calibration from my monitor in Windows.  So it knows
the gamma of both the display and scanner.  Why does it still end up
wrong?  Is this a bug in Leica's software or do I not understand
something?

As an aside, I googled this imaging core and Aperio, and it brings up
a lot of papers with badly oversaturated slides, so I'm pretty sure
this isn't just me.

Mike

On Mon, Apr 6, 2015 at 7:18 PM, Armstrong, Brian <[hidden email]> wrote:

> Hello Mike, I believe that some scanners use a default gamma setting of 0.45 for BF imaging. If this is the case then with the gamma at 1.0 it will appear oversaturated. Take a look at your gamma settings on Aperio Image Scope and see where it is set. Try the gamma at 0.45 and see how it looks. Ask your imaging partner what the gamma setting is on the Aperio scanner.
>
> Cheers,
>
> Brian Armstrong PhD
> Director, Light Microscopy Core
> Beckman  Research Institute
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michael Giacomelli
> Sent: Monday, April 06, 2015 4:02 PM
> To: [hidden email]
> Subject: Leica slide scanner calibration
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> I had some pathology slides scanned at a local imaging core on an Aperio scanner, but the color appears to be quite off.  Using the built in correction in the aperio visualization software (which I believe uses the correction information from the scanner), my H&E slides are kind of a hot, oversaturated pink.  Disabling it brings it closer to reality, but its still much too saturated.  Just to convince myself, I looked side by side between the scanned images and the original slides and used a second monitor.  Something is wrong.
>
> I don't think this is my monitor, its an 8 bit IPS panel thats been color calibrated to ~100% sRGB using an X-Rite.  Besides giving excellent accuracy in the X-Rite measurements, other images look fine.
>
> My assumption is that it has to be the scanner itself.  Has anyone had this problem before?  I'm going to go back to the imaging core and try to talk to them about it, but I was hoping to find out a little bit more about the problem so I don't sound clueless when I say that my images look 'funny'.
>
> Mike
>
>
> ---------------------------------------------------------------------
> *SECURITY/CONFIDENTIALITY WARNING:
> This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p)
> ---------------------------------------------------------------------
>

[Michael Giacomelli]

*****
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*****

I wonder if anyone has tried color calibrating a histology slide
scanner?  I know they make kits for photography film scanners, but I'm
not sure if that would work here.  Measuring the transfer function
from the scanner and mapping onto sRGB would be the safest way to
proceed I think.

Mike

On Tue, Apr 7, 2015 at 10:45 AM, Michael Giacomelli <[hidden email]> wrote:

> Hi Brian,
>
> I'm a little surprised that this is an issue, but I think you may be
> right.  Adjusting the gamma by approximately that amount makes the
> images look better. I'm not certain they're correct, but its certainly
> much better.
>
> A question though:  why is this even a problem?  As I understand it,
> the Aperio format includes color calibration information from the
> scanner (theres an option to apply it in their software), and it will
> take the color calibration from my monitor in Windows.  So it knows
> the gamma of both the display and scanner.  Why does it still end up
> wrong?  Is this a bug in Leica's software or do I not understand
> something?
>
> As an aside, I googled this imaging core and Aperio, and it brings up
> a lot of papers with badly oversaturated slides, so I'm pretty sure
> this isn't just me.
>
> Mike
>
> On Mon, Apr 6, 2015 at 7:18 PM, Armstrong, Brian <[hidden email]> wrote:
>> Hello Mike, I believe that some scanners use a default gamma setting of 0.45 for BF imaging. If this is the case then with the gamma at 1.0 it will appear oversaturated. Take a look at your gamma settings on Aperio Image Scope and see where it is set. Try the gamma at 0.45 and see how it looks. Ask your imaging partner what the gamma setting is on the Aperio scanner.
>>
>> Cheers,
>>
>> Brian Armstrong PhD
>> Director, Light Microscopy Core
>> Beckman  Research Institute
>>
>>
>>
>> -----Original Message-----
>> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michael Giacomelli
>> Sent: Monday, April 06, 2015 4:02 PM
>> To: [hidden email]
>> Subject: Leica slide scanner calibration
>>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> I had some pathology slides scanned at a local imaging core on an Aperio scanner, but the color appears to be quite off.  Using the built in correction in the aperio visualization software (which I believe uses the correction information from the scanner), my H&E slides are kind of a hot, oversaturated pink.  Disabling it brings it closer to reality, but its still much too saturated.  Just to convince myself, I looked side by side between the scanned images and the original slides and used a second monitor.  Something is wrong.
>>
>> I don't think this is my monitor, its an 8 bit IPS panel thats been color calibrated to ~100% sRGB using an X-Rite.  Besides giving excellent accuracy in the X-Rite measurements, other images look fine.
>>
>> My assumption is that it has to be the scanner itself.  Has anyone had this problem before?  I'm going to go back to the imaging core and try to talk to them about it, but I was hoping to find out a little bit more about the problem so I don't sound clueless when I say that my images look 'funny'.
>>
>> Mike
>>
>>
>> ---------------------------------------------------------------------
>> *SECURITY/CONFIDENTIALITY WARNING:
>> This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p)
>> ---------------------------------------------------------------------
>>

[Armstrong, Brian]

Hi Mike, I know that the Hamamatsu Nanozoomer comes with an RGB calibration slide and a "program" for calibrating the system.
 
Cheers,

Brian Armstrong PhD
Director, Light Microscopy Core
Beckman  Research Institute



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michael Giacomelli
Sent: Tuesday, April 07, 2015 9:59 AM
To: [hidden email]
Subject: Re: Leica slide scanner calibration

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

I wonder if anyone has tried color calibrating a histology slide scanner?  I know they make kits for photography film scanners, but I'm not sure if that would work here.  Measuring the transfer function from the scanner and mapping onto sRGB would be the safest way to proceed I think.

Mike

On Tue, Apr 7, 2015 at 10:45 AM, Michael Giacomelli <[hidden email]> wrote:

> Hi Brian,
>
> I'm a little surprised that this is an issue, but I think you may be
> right.  Adjusting the gamma by approximately that amount makes the
> images look better. I'm not certain they're correct, but its certainly
> much better.
>
> A question though:  why is this even a problem?  As I understand it,
> the Aperio format includes color calibration information from the
> scanner (theres an option to apply it in their software), and it will
> take the color calibration from my monitor in Windows.  So it knows
> the gamma of both the display and scanner.  Why does it still end up
> wrong?  Is this a bug in Leica's software or do I not understand
> something?
>
> As an aside, I googled this imaging core and Aperio, and it brings up
> a lot of papers with badly oversaturated slides, so I'm pretty sure
> this isn't just me.
>
> Mike
>
> On Mon, Apr 6, 2015 at 7:18 PM, Armstrong, Brian <[hidden email]> wrote:
>> Hello Mike, I believe that some scanners use a default gamma setting of 0.45 for BF imaging. If this is the case then with the gamma at 1.0 it will appear oversaturated. Take a look at your gamma settings on Aperio Image Scope and see where it is set. Try the gamma at 0.45 and see how it looks. Ask your imaging partner what the gamma setting is on the Aperio scanner.
>>
>> Cheers,
>>
>> Brian Armstrong PhD
>> Director, Light Microscopy Core
>> Beckman  Research Institute
>>
>>
>>
>> -----Original Message-----
>> From: Confocal Microscopy List
>> [mailto:[hidden email]] On Behalf Of Michael
>> Giacomelli
>> Sent: Monday, April 06, 2015 4:02 PM
>> To: [hidden email]
>> Subject: Leica slide scanner calibration
>>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> I had some pathology slides scanned at a local imaging core on an Aperio scanner, but the color appears to be quite off.  Using the built in correction in the aperio visualization software (which I believe uses the correction information from the scanner), my H&E slides are kind of a hot, oversaturated pink.  Disabling it brings it closer to reality, but its still much too saturated.  Just to convince myself, I looked side by side between the scanned images and the original slides and used a second monitor.  Something is wrong.
>>
>> I don't think this is my monitor, its an 8 bit IPS panel thats been color calibrated to ~100% sRGB using an X-Rite.  Besides giving excellent accuracy in the X-Rite measurements, other images look fine.
>>
>> My assumption is that it has to be the scanner itself.  Has anyone had this problem before?  I'm going to go back to the imaging core and try to talk to them about it, but I was hoping to find out a little bit more about the problem so I don't sound clueless when I say that my images look 'funny'.
>>
>> Mike
>>
>>
>> ---------------------------------------------------------------------
>> *SECURITY/CONFIDENTIALITY WARNING:
>> This message and any attachments are intended solely for the
>> individual or entity to which they are addressed. This communication
>> may contain information that is privileged, confidential, or exempt
>> from disclosure under applicable law (e.g., personal health
>> information, research data, financial information). Because this
>> e-mail has been sent without encryption, individuals other than the
>> intended recipient may be able to view the information, forward it to
>> others or tamper with the information without the knowledge or
>> consent of the sender. If you are not the intended recipient, or the
>> employee or person responsible for delivering the message to the
>> intended recipient, any dissemination, distribution or copying of the
>> communication is strictly prohibited. If you received the
>> communication in error, please notify the sender immediately by
>> replying to this message and deleting the message and any
>> accompanying files from your system. If, due to the security risks,
>> you do not wish to receive further communications via e-mail, please
>> reply to this message and inform the sender that you do not wish to
>> receive further e-mail from the sender. (fpc5p)
>> ---------------------------------------------------------------------
>>

[Sathya]

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Hi Mike,
ChromaCal from datacolor (www.chromacal.com) has a color calibration slide and a monitor calibration kit (No commercial interest). Seems to be a fantastic way to proceed with bright field imaging. There was a publication using the ChromaCal calibration system recently in: Journal of Histochemistry and Cytochemistry 2015, Vol. 63 (4): 233-243 titled "An Innovative Method for Obtaining Consistent Images and Quantification of Histochemically Stained Specimens" authored by Michael A. Linden, Gerald J. Sedgewick and Marna Ericson. Good luck.
 
Sathya Srinivasan
Manager
RUN Advanced Optical Microscopy Facility
(www.ucalgary.ca/runcore)
University of Calgary
Calgary, Alberta, Canada
 

> Date: Tue, 7 Apr 2015 11:01:59 -0700
> From: [hidden email]
> Subject: Re: Leica slide scanner calibration
> To: [hidden email]
>
> Hi Mike, I know that the Hamamatsu Nanozoomer comes with an RGB calibration slide and a "program" for calibrating the system.
>  
> Cheers,
>
> Brian Armstrong PhD
> Director, Light Microscopy Core
> Beckman  Research Institute
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michael Giacomelli
> Sent: Tuesday, April 07, 2015 9:59 AM
> To: [hidden email]
> Subject: Re: Leica slide scanner calibration
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> I wonder if anyone has tried color calibrating a histology slide scanner?  I know they make kits for photography film scanners, but I'm not sure if that would work here.  Measuring the transfer function from the scanner and mapping onto sRGB would be the safest way to proceed I think.
>
> Mike
>
> On Tue, Apr 7, 2015 at 10:45 AM, Michael Giacomelli <[hidden email]> wrote:
> > Hi Brian,
> >
> > I'm a little surprised that this is an issue, but I think you may be
> > right.  Adjusting the gamma by approximately that amount makes the
> > images look better. I'm not certain they're correct, but its certainly
> > much better.
> >
> > A question though:  why is this even a problem?  As I understand it,
> > the Aperio format includes color calibration information from the
> > scanner (theres an option to apply it in their software), and it will
> > take the color calibration from my monitor in Windows.  So it knows
> > the gamma of both the display and scanner.  Why does it still end up
> > wrong?  Is this a bug in Leica's software or do I not understand
> > something?
> >
> > As an aside, I googled this imaging core and Aperio, and it brings up
> > a lot of papers with badly oversaturated slides, so I'm pretty sure
> > this isn't just me.
> >
> > Mike
> >
> > On Mon, Apr 6, 2015 at 7:18 PM, Armstrong, Brian <[hidden email]> wrote:
> >> Hello Mike, I believe that some scanners use a default gamma setting of 0.45 for BF imaging. If this is the case then with the gamma at 1.0 it will appear oversaturated. Take a look at your gamma settings on Aperio Image Scope and see where it is set. Try the gamma at 0.45 and see how it looks. Ask your imaging partner what the gamma setting is on the Aperio scanner.
> >>
> >> Cheers,
> >>
> >> Brian Armstrong PhD
> >> Director, Light Microscopy Core
> >> Beckman  Research Institute
> >>
> >>
> >>
> >> -----Original Message-----
> >> From: Confocal Microscopy List
> >> [mailto:[hidden email]] On Behalf Of Michael
> >> Giacomelli
> >> Sent: Monday, April 06, 2015 4:02 PM
> >> To: [hidden email]
> >> Subject: Leica slide scanner calibration
> >>
> >> *****
> >> To join, leave or search the confocal microscopy listserv, go to:
> >> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> >> Post images on http://www.imgur.com and include the link in your posting.
> >> *****
> >>
> >> I had some pathology slides scanned at a local imaging core on an Aperio scanner, but the color appears to be quite off.  Using the built in correction in the aperio visualization software (which I believe uses the correction information from the scanner), my H&E slides are kind of a hot, oversaturated pink.  Disabling it brings it closer to reality, but its still much too saturated.  Just to convince myself, I looked side by side between the scanned images and the original slides and used a second monitor.  Something is wrong.
> >>
> >> I don't think this is my monitor, its an 8 bit IPS panel thats been color calibrated to ~100% sRGB using an X-Rite.  Besides giving excellent accuracy in the X-Rite measurements, other images look fine.
> >>
> >> My assumption is that it has to be the scanner itself.  Has anyone had this problem before?  I'm going to go back to the imaging core and try to talk to them about it, but I was hoping to find out a little bit more about the problem so I don't sound clueless when I say that my images look 'funny'.
> >>
> >> Mike
> >>
> >>
> >> ---------------------------------------------------------------------
> >> *SECURITY/CONFIDENTIALITY WARNING:
> >> This message and any attachments are intended solely for the
> >> individual or entity to which they are addressed. This communication
> >> may contain information that is privileged, confidential, or exempt
> >> from disclosure under applicable law (e.g., personal health
> >> information, research data, financial information). Because this
> >> e-mail has been sent without encryption, individuals other than the
> >> intended recipient may be able to view the information, forward it to
> >> others or tamper with the information without the knowledge or
> >> consent of the sender. If you are not the intended recipient, or the
> >> employee or person responsible for delivering the message to the
> >> intended recipient, any dissemination, distribution or copying of the
> >> communication is strictly prohibited. If you received the
> >> communication in error, please notify the sender immediately by
> >> replying to this message and deleting the message and any
> >> accompanying files from your system. If, due to the security risks,
> >> you do not wish to receive further communications via e-mail, please
> >> reply to this message and inform the sender that you do not wish to
> >> receive further e-mail from the sender. (fpc5p)
> >> ---------------------------------------------------------------------
> >>

     

[George McNamara]

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*****

Hi Michael,
I have been using Pathscan Enabler slide scanners since 2000 - no
calibration issues with any of the models. I (our lab) currently has
http://meyerinst.com/scanners/pathscan-enabler-iv/
and the vendor has a new model
http://meyerinst.com/pathscan-enabler-5/
and even more fun looking is  
http://meyerinst.com/gigamacro-gigapixel-macro-imaging/
and
https://www.youtube.com/watch?v=uY7w8ZSmNHE&feature=youtu.be

Tiki_Goddess was acquired on an original Pathscan Enabler (Polaroid 35
mm film scanner with microscope adapter)
http://home.earthlink.net/~tiki_goddess/TikiGoddess.jpg
backstory at
http://home.earthlink.net/~tiki_goddess

Hamamatsu NanoZoomer scan is available at
http://works.bepress.com/gmcnamara/11/


See also my 2005 Color Balancing Histology Images article, available at
http://home.earthlink.net/~geomcnamara/McNamara2005JoH28n2pp81-88.pdf
Photoshop settings can be stored and reused with Actions - my thanks to
Jerry Sedgewick for emphasizing this,
http://www.amazon.com/Scientific-Imaging-Photoshop-Methods-Measurement/dp/0321514335
See also   http://www.imagingandanalysis.com/   ... and Jerry does
consulting and onsite training. Jerry is also into imaging ethics, which
leads me to segway to ...

According to two identical notices in the March issue of /Genes &
Development,/ the alleged retraction in/ Cell/ came about “because
original data were compiled from different replicate experiments in
order to assemble certain figure panels. As the same analytical
methodology was used in this [/Genes & Development/] manuscript, we
believe that the responsible course of action is to retract the article.”
http://www.the-scientist.com/?articles.view/articleNo/42503/title/Three-Retractions-for-Highly-Cited-Author/
http://retractionwatch.com/2015/04/03/other-shoe-drops-for-mit-cancer-researcher-robert-weinberg-as-cell-retraction-appears/ 


Upshot: present data (whether microscopy or blots or other) correctly.

Enjoy,

George
p.s. Aperio support is at
http://www.leicabiosystems.com/pathology-imaging/aperio-epathology/



On 4/7/2015 11:59 AM, Michael Giacomelli wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> I wonder if anyone has tried color calibrating a histology slide
> scanner?  I know they make kits for photography film scanners, but I'm
> not sure if that would work here.  Measuring the transfer function
> from the scanner and mapping onto sRGB would be the safest way to
> proceed I think.
>
> Mike
>
> On Tue, Apr 7, 2015 at 10:45 AM, Michael Giacomelli<[hidden email]>  wrote:
>    
>> Hi Brian,
>>
>> I'm a little surprised that this is an issue, but I think you may be
>> right.  Adjusting the gamma by approximately that amount makes the
>> images look better. I'm not certain they're correct, but its certainly
>> much better.
>>
>> A question though:  why is this even a problem?  As I understand it,
>> the Aperio format includes color calibration information from the
>> scanner (theres an option to apply it in their software), and it will
>> take the color calibration from my monitor in Windows.  So it knows
>> the gamma of both the display and scanner.  Why does it still end up
>> wrong?  Is this a bug in Leica's software or do I not understand
>> something?
>>
>> As an aside, I googled this imaging core and Aperio, and it brings up
>> a lot of papers with badly oversaturated slides, so I'm pretty sure
>> this isn't just me.
>>
>> Mike
>>
>> On Mon, Apr 6, 2015 at 7:18 PM, Armstrong, Brian<[hidden email]>  wrote:
>>      
>>> Hello Mike, I believe that some scanners use a default gamma setting of 0.45 for BF imaging. If this is the case then with the gamma at 1.0 it will appear oversaturated. Take a look at your gamma settings on Aperio Image Scope and see where it is set. Try the gamma at 0.45 and see how it looks. Ask your imaging partner what the gamma setting is on the Aperio scanner.
>>>
>>> Cheers,
>>>
>>> Brian Armstrong PhD
>>> Director, Light Microscopy Core
>>> Beckman  Research Institute
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Michael Giacomelli
>>> Sent: Monday, April 06, 2015 4:02 PM
>>> To: [hidden email]
>>> Subject: Leica slide scanner calibration
>>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> Post images on http://www.imgur.com and include the link in your posting.
>>> *****
>>>
>>> I had some pathology slides scanned at a local imaging core on an Aperio scanner, but the color appears to be quite off.  Using the built in correction in the aperio visualization software (which I believe uses the correction information from the scanner), my H&E slides are kind of a hot, oversaturated pink.  Disabling it brings it closer to reality, but its still much too saturated.  Just to convince myself, I looked side by side between the scanned images and the original slides and used a second monitor.  Something is wrong.
>>>
>>> I don't think this is my monitor, its an 8 bit IPS panel thats been color calibrated to ~100% sRGB using an X-Rite.  Besides giving excellent accuracy in the X-Rite measurements, other images look fine.
>>>
>>> My assumption is that it has to be the scanner itself.  Has anyone had this problem before?  I'm going to go back to the imaging core and try to talk to them about it, but I was hoping to find out a little bit more about the problem so I don't sound clueless when I say that my images look 'funny'.
>>>
>>> Mike
>>>
>>>
>>> ---------------------------------------------------------------------
>>> *SECURITY/CONFIDENTIALITY WARNING:
>>> This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p)
>>> ---------------------------------------------------------------------
>>>
>>>        
>    

--



George McNamara, Ph.D.
Single Cells Analyst
L.J.N. Cooper Lab
University of Texas M.D. Anderson Cancer Center
Houston, TX 77054
Tattletales http://works.bepress.com/gmcnamara/42

[Michael Giacomelli]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

I've forwarded comparison images between a Phillips scanner I borrowed
access to and our core facility's Aperio to Leica.  Their initial
reaction is that something is very wrong, but I'm waiting to hear back
from an engineer there.  Hopefully this is something that can be
fixed.

Somewhat troubling to me though is that no one I've spoken to has been
able to tell me how the colorspace on the scanner is actually
calibrated.  I expected them to use reference slides, much like you
would calibrate a digital camera.  Its a little troubling to me that
people do not seem to know, since I would expect a scanner to need
semi-regular recalibration (and not just white balancing) as bulbs or
diodes age.

Mike

On Tue, Apr 7, 2015 at 7:08 PM, George McNamara
<[hidden email]> wrote:

> Hi Michael,
> I have been using Pathscan Enabler slide scanners since 2000 - no
> calibration issues with any of the models. I (our lab) currently has
> http://meyerinst.com/scanners/pathscan-enabler-iv/
> and the vendor has a new model
> http://meyerinst.com/pathscan-enabler-5/
> and even more fun looking is
> http://meyerinst.com/gigamacro-gigapixel-macro-imaging/
> and
> https://www.youtube.com/watch?v=uY7w8ZSmNHE&feature=youtu.be
>
> Tiki_Goddess was acquired on an original Pathscan Enabler (Polaroid 35 mm
> film scanner with microscope adapter)
> http://home.earthlink.net/~tiki_goddess/TikiGoddess.jpg
> backstory at
> http://home.earthlink.net/~tiki_goddess
>
> Hamamatsu NanoZoomer scan is available at
> http://works.bepress.com/gmcnamara/11/
>
>
> See also my 2005 Color Balancing Histology Images article, available at
> http://home.earthlink.net/~geomcnamara/McNamara2005JoH28n2pp81-88.pdf
> Photoshop settings can be stored and reused with Actions - my thanks to
> Jerry Sedgewick for emphasizing this,
> http://www.amazon.com/Scientific-Imaging-Photoshop-Methods-Measurement/dp/0321514335
> See also   http://www.imagingandanalysis.com/   ... and Jerry does
> consulting and onsite training. Jerry is also into imaging ethics, which
> leads me to segway to ...
>
> According to two identical notices in the March issue of Genes &
> Development, the alleged retraction in Cell came about “because original
> data were compiled from different replicate experiments in order to assemble
> certain figure panels. As the same analytical methodology was used in this
> [Genes & Development] manuscript, we believe that the responsible course of
> action is to retract the article.”
> http://www.the-scientist.com/?articles.view/articleNo/42503/title/Three-Retractions-for-Highly-Cited-Author/
> http://retractionwatch.com/2015/04/03/other-shoe-drops-for-mit-cancer-researcher-robert-weinberg-as-cell-retraction-appears/
>
> Upshot: present data (whether microscopy or blots or other) correctly.
>
> Enjoy,
>
> George
> p.s. Aperio support is at
> http://www.leicabiosystems.com/pathology-imaging/aperio-epathology/
>
>
>
>
> On 4/7/2015 11:59 AM, Michael Giacomelli wrote:
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> I wonder if anyone has tried color calibrating a histology slide
> scanner?  I know they make kits for photography film scanners, but I'm
> not sure if that would work here.  Measuring the transfer function
> from the scanner and mapping onto sRGB would be the safest way to
> proceed I think.
>
> Mike
>
> On Tue, Apr 7, 2015 at 10:45 AM, Michael Giacomelli <[hidden email]> wrote:
>
>
> Hi Brian,
>
> I'm a little surprised that this is an issue, but I think you may be
> right.  Adjusting the gamma by approximately that amount makes the
> images look better. I'm not certain they're correct, but its certainly
> much better.
>
> A question though:  why is this even a problem?  As I understand it,
> the Aperio format includes color calibration information from the
> scanner (theres an option to apply it in their software), and it will
> take the color calibration from my monitor in Windows.  So it knows
> the gamma of both the display and scanner.  Why does it still end up
> wrong?  Is this a bug in Leica's software or do I not understand
> something?
>
> As an aside, I googled this imaging core and Aperio, and it brings up
> a lot of papers with badly oversaturated slides, so I'm pretty sure
> this isn't just me.
>
> Mike
>
> On Mon, Apr 6, 2015 at 7:18 PM, Armstrong, Brian <[hidden email]> wrote:
>
>
> Hello Mike, I believe that some scanners use a default gamma setting of 0.45
> for BF imaging. If this is the case then with the gamma at 1.0 it will
> appear oversaturated. Take a look at your gamma settings on Aperio Image
> Scope and see where it is set. Try the gamma at 0.45 and see how it looks.
> Ask your imaging partner what the gamma setting is on the Aperio scanner.
>
> Cheers,
>
> Brian Armstrong PhD
> Director, Light Microscopy Core
> Beckman  Research Institute
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On
> Behalf Of Michael Giacomelli
> Sent: Monday, April 06, 2015 4:02 PM
> To: [hidden email]
> Subject: Leica slide scanner calibration
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> I had some pathology slides scanned at a local imaging core on an Aperio
> scanner, but the color appears to be quite off.  Using the built in
> correction in the aperio visualization software (which I believe uses the
> correction information from the scanner), my H&E slides are kind of a hot,
> oversaturated pink.  Disabling it brings it closer to reality, but its still
> much too saturated.  Just to convince myself, I looked side by side between
> the scanned images and the original slides and used a second monitor.
> Something is wrong.
>
> I don't think this is my monitor, its an 8 bit IPS panel thats been color
> calibrated to ~100% sRGB using an X-Rite.  Besides giving excellent accuracy
> in the X-Rite measurements, other images look fine.
>
> My assumption is that it has to be the scanner itself.  Has anyone had this
> problem before?  I'm going to go back to the imaging core and try to talk to
> them about it, but I was hoping to find out a little bit more about the
> problem so I don't sound clueless when I say that my images look 'funny'.
>
> Mike
>
>
> ---------------------------------------------------------------------
> *SECURITY/CONFIDENTIALITY WARNING:
> This message and any attachments are intended solely for the individual or
> entity to which they are addressed. This communication may contain
> information that is privileged, confidential, or exempt from disclosure
> under applicable law (e.g., personal health information, research data,
> financial information). Because this e-mail has been sent without
> encryption, individuals other than the intended recipient may be able to
> view the information, forward it to others or tamper with the information
> without the knowledge or consent of the sender. If you are not the intended
> recipient, or the employee or person responsible for delivering the message
> to the intended recipient, any dissemination, distribution or copying of the
> communication is strictly prohibited. If you received the communication in
> error, please notify the sender immediately by replying to this message and
> deleting the message and any accompanying files from your system. If, due to
> the security risks, you do not wi
> sh to receive further communications via e-mail, please reply to this
> message and inform the sender that you do not wish to receive further e-mail
> from the sender. (fpc5p)
> ---------------------------------------------------------------------
>
>
>
>
>
>
>
> --
>
>
>
> George McNamara, Ph.D.
> Single Cells Analyst
> L.J.N. Cooper Lab
> University of Texas M.D. Anderson Cancer Center
> Houston, TX 77054
> Tattletales http://works.bepress.com/gmcnamara/42

[Michael Giacomelli]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

After a lot of emails, I did manage to get ahold of someone at Leica
familiar with the Aperio scanners who is helping me understand the
calibration problems with our core's scanner.

I'll update the list if we come up with a solution.

Mike

On Wed, Apr 8, 2015 at 1:26 PM, Michael Giacomelli <[hidden email]> wrote:

> I've forwarded comparison images between a Phillips scanner I borrowed
> access to and our core facility's Aperio to Leica.  Their initial
> reaction is that something is very wrong, but I'm waiting to hear back
> from an engineer there.  Hopefully this is something that can be
> fixed.
>
> Somewhat troubling to me though is that no one I've spoken to has been
> able to tell me how the colorspace on the scanner is actually
> calibrated.  I expected them to use reference slides, much like you
> would calibrate a digital camera.  Its a little troubling to me that
> people do not seem to know, since I would expect a scanner to need
> semi-regular recalibration (and not just white balancing) as bulbs or
> diodes age.
>
> Mike
>
> On Tue, Apr 7, 2015 at 7:08 PM, George McNamara
> <[hidden email]> wrote:
>> Hi Michael,
>> I have been using Pathscan Enabler slide scanners since 2000 - no
>> calibration issues with any of the models. I (our lab) currently has
>> http://meyerinst.com/scanners/pathscan-enabler-iv/
>> and the vendor has a new model
>> http://meyerinst.com/pathscan-enabler-5/
>> and even more fun looking is
>> http://meyerinst.com/gigamacro-gigapixel-macro-imaging/
>> and
>> https://www.youtube.com/watch?v=uY7w8ZSmNHE&feature=youtu.be
>>
>> Tiki_Goddess was acquired on an original Pathscan Enabler (Polaroid 35 mm
>> film scanner with microscope adapter)
>> http://home.earthlink.net/~tiki_goddess/TikiGoddess.jpg
>> backstory at
>> http://home.earthlink.net/~tiki_goddess
>>
>> Hamamatsu NanoZoomer scan is available at
>> http://works.bepress.com/gmcnamara/11/
>>
>>
>> See also my 2005 Color Balancing Histology Images article, available at
>> http://home.earthlink.net/~geomcnamara/McNamara2005JoH28n2pp81-88.pdf
>> Photoshop settings can be stored and reused with Actions - my thanks to
>> Jerry Sedgewick for emphasizing this,
>> http://www.amazon.com/Scientific-Imaging-Photoshop-Methods-Measurement/dp/0321514335
>> See also   http://www.imagingandanalysis.com/   ... and Jerry does
>> consulting and onsite training. Jerry is also into imaging ethics, which
>> leads me to segway to ...
>>
>> According to two identical notices in the March issue of Genes &
>> Development, the alleged retraction in Cell came about “because original
>> data were compiled from different replicate experiments in order to assemble
>> certain figure panels. As the same analytical methodology was used in this
>> [Genes & Development] manuscript, we believe that the responsible course of
>> action is to retract the article.”
>> http://www.the-scientist.com/?articles.view/articleNo/42503/title/Three-Retractions-for-Highly-Cited-Author/
>> http://retractionwatch.com/2015/04/03/other-shoe-drops-for-mit-cancer-researcher-robert-weinberg-as-cell-retraction-appears/
>>
>> Upshot: present data (whether microscopy or blots or other) correctly.
>>
>> Enjoy,
>>
>> George
>> p.s. Aperio support is at
>> http://www.leicabiosystems.com/pathology-imaging/aperio-epathology/
>>
>>
>>
>>
>> On 4/7/2015 11:59 AM, Michael Giacomelli wrote:
>>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> I wonder if anyone has tried color calibrating a histology slide
>> scanner?  I know they make kits for photography film scanners, but I'm
>> not sure if that would work here.  Measuring the transfer function
>> from the scanner and mapping onto sRGB would be the safest way to
>> proceed I think.
>>
>> Mike
>>
>> On Tue, Apr 7, 2015 at 10:45 AM, Michael Giacomelli <[hidden email]> wrote:
>>
>>
>> Hi Brian,
>>
>> I'm a little surprised that this is an issue, but I think you may be
>> right.  Adjusting the gamma by approximately that amount makes the
>> images look better. I'm not certain they're correct, but its certainly
>> much better.
>>
>> A question though:  why is this even a problem?  As I understand it,
>> the Aperio format includes color calibration information from the
>> scanner (theres an option to apply it in their software), and it will
>> take the color calibration from my monitor in Windows.  So it knows
>> the gamma of both the display and scanner.  Why does it still end up
>> wrong?  Is this a bug in Leica's software or do I not understand
>> something?
>>
>> As an aside, I googled this imaging core and Aperio, and it brings up
>> a lot of papers with badly oversaturated slides, so I'm pretty sure
>> this isn't just me.
>>
>> Mike
>>
>> On Mon, Apr 6, 2015 at 7:18 PM, Armstrong, Brian <[hidden email]> wrote:
>>
>>
>> Hello Mike, I believe that some scanners use a default gamma setting of 0.45
>> for BF imaging. If this is the case then with the gamma at 1.0 it will
>> appear oversaturated. Take a look at your gamma settings on Aperio Image
>> Scope and see where it is set. Try the gamma at 0.45 and see how it looks.
>> Ask your imaging partner what the gamma setting is on the Aperio scanner.
>>
>> Cheers,
>>
>> Brian Armstrong PhD
>> Director, Light Microscopy Core
>> Beckman  Research Institute
>>
>>
>>
>> -----Original Message-----
>> From: Confocal Microscopy List [mailto:[hidden email]] On
>> Behalf Of Michael Giacomelli
>> Sent: Monday, April 06, 2015 4:02 PM
>> To: [hidden email]
>> Subject: Leica slide scanner calibration
>>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> I had some pathology slides scanned at a local imaging core on an Aperio
>> scanner, but the color appears to be quite off.  Using the built in
>> correction in the aperio visualization software (which I believe uses the
>> correction information from the scanner), my H&E slides are kind of a hot,
>> oversaturated pink.  Disabling it brings it closer to reality, but its still
>> much too saturated.  Just to convince myself, I looked side by side between
>> the scanned images and the original slides and used a second monitor.
>> Something is wrong.
>>
>> I don't think this is my monitor, its an 8 bit IPS panel thats been color
>> calibrated to ~100% sRGB using an X-Rite.  Besides giving excellent accuracy
>> in the X-Rite measurements, other images look fine.
>>
>> My assumption is that it has to be the scanner itself.  Has anyone had this
>> problem before?  I'm going to go back to the imaging core and try to talk to
>> them about it, but I was hoping to find out a little bit more about the
>> problem so I don't sound clueless when I say that my images look 'funny'.
>>
>> Mike
>>
>>
>> ---------------------------------------------------------------------
>> *SECURITY/CONFIDENTIALITY WARNING:
>> This message and any attachments are intended solely for the individual or
>> entity to which they are addressed. This communication may contain
>> information that is privileged, confidential, or exempt from disclosure
>> under applicable law (e.g., personal health information, research data,
>> financial information). Because this e-mail has been sent without
>> encryption, individuals other than the intended recipient may be able to
>> view the information, forward it to others or tamper with the information
>> without the knowledge or consent of the sender. If you are not the intended
>> recipient, or the employee or person responsible for delivering the message
>> to the intended recipient, any dissemination, distribution or copying of the
>> communication is strictly prohibited. If you received the communication in
>> error, please notify the sender immediately by replying to this message and
>> deleting the message and any accompanying files from your system. If, due to
>> the security risks, you do not wi
>> sh to receive further communications via e-mail, please reply to this
>> message and inform the sender that you do not wish to receive further e-mail
>> from the sender. (fpc5p)
>> ---------------------------------------------------------------------
>>
>>
>>
>>
>>
>>
>>
>> --
>>
>>
>>
>> George McNamara, Ph.D.
>> Single Cells Analyst
>> L.J.N. Cooper Lab
>> University of Texas M.D. Anderson Cancer Center
>> Houston, TX 77054
>> Tattletales http://works.bepress.com/gmcnamara/42

[Michael Giacomelli]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

After a lot of runaround, I got to the bottom of this issue.
According to Leica, the Aperio scanner's color correction is set to
produce more appealing looking images and so it "enhances" colors, but
it does not reproduce what you would see in a microscope.  Apparently
we could buy a newer scanner if we want accurate images.  This would
explain why disabling all color correction actually produces a better
(but still inaccurate) image: what looks like miscalibration to me is
considered an undocumented image enhancement feature.  Annoyingly,
they initially told me that the color correction took into account the
device calibration.  This (and the manual) is apparently incorrect, at
least for our scanner.  They remembered otherwise after a lengthy
exchange.

At this point I could try to calibrate and fix in post processing, but
I'm disturbed enough that Leica would silently alter my images that I
don't think I want to take a chance with them again.  From what I've
seen, the Phillips scanners ship with very good calibration.

Mike

On Wed, Apr 15, 2015 at 5:48 PM, Michael Giacomelli <[hidden email]> wrote:

> After a lot of emails, I did manage to get ahold of someone at Leica
> familiar with the Aperio scanners who is helping me understand the
> calibration problems with our core's scanner.
>
> I'll update the list if we come up with a solution.
>
> Mike
>
> On Wed, Apr 8, 2015 at 1:26 PM, Michael Giacomelli <[hidden email]> wrote:
>> I've forwarded comparison images between a Phillips scanner I borrowed
>> access to and our core facility's Aperio to Leica.  Their initial
>> reaction is that something is very wrong, but I'm waiting to hear back
>> from an engineer there.  Hopefully this is something that can be
>> fixed.
>>
>> Somewhat troubling to me though is that no one I've spoken to has been
>> able to tell me how the colorspace on the scanner is actually
>> calibrated.  I expected them to use reference slides, much like you
>> would calibrate a digital camera.  Its a little troubling to me that
>> people do not seem to know, since I would expect a scanner to need
>> semi-regular recalibration (and not just white balancing) as bulbs or
>> diodes age.
>>
>> Mike
>>
>> On Tue, Apr 7, 2015 at 7:08 PM, George McNamara
>> <[hidden email]> wrote:
>>> Hi Michael,
>>> I have been using Pathscan Enabler slide scanners since 2000 - no
>>> calibration issues with any of the models. I (our lab) currently has
>>> http://meyerinst.com/scanners/pathscan-enabler-iv/
>>> and the vendor has a new model
>>> http://meyerinst.com/pathscan-enabler-5/
>>> and even more fun looking is
>>> http://meyerinst.com/gigamacro-gigapixel-macro-imaging/
>>> and
>>> https://www.youtube.com/watch?v=uY7w8ZSmNHE&feature=youtu.be
>>>
>>> Tiki_Goddess was acquired on an original Pathscan Enabler (Polaroid 35 mm
>>> film scanner with microscope adapter)
>>> http://home.earthlink.net/~tiki_goddess/TikiGoddess.jpg
>>> backstory at
>>> http://home.earthlink.net/~tiki_goddess
>>>
>>> Hamamatsu NanoZoomer scan is available at
>>> http://works.bepress.com/gmcnamara/11/
>>>
>>>
>>> See also my 2005 Color Balancing Histology Images article, available at
>>> http://home.earthlink.net/~geomcnamara/McNamara2005JoH28n2pp81-88.pdf
>>> Photoshop settings can be stored and reused with Actions - my thanks to
>>> Jerry Sedgewick for emphasizing this,
>>> http://www.amazon.com/Scientific-Imaging-Photoshop-Methods-Measurement/dp/0321514335
>>> See also   http://www.imagingandanalysis.com/   ... and Jerry does
>>> consulting and onsite training. Jerry is also into imaging ethics, which
>>> leads me to segway to ...
>>>
>>> According to two identical notices in the March issue of Genes &
>>> Development, the alleged retraction in Cell came about “because original
>>> data were compiled from different replicate experiments in order to assemble
>>> certain figure panels. As the same analytical methodology was used in this
>>> [Genes & Development] manuscript, we believe that the responsible course of
>>> action is to retract the article.”
>>> http://www.the-scientist.com/?articles.view/articleNo/42503/title/Three-Retractions-for-Highly-Cited-Author/
>>> http://retractionwatch.com/2015/04/03/other-shoe-drops-for-mit-cancer-researcher-robert-weinberg-as-cell-retraction-appears/
>>>
>>> Upshot: present data (whether microscopy or blots or other) correctly.
>>>
>>> Enjoy,
>>>
>>> George
>>> p.s. Aperio support is at
>>> http://www.leicabiosystems.com/pathology-imaging/aperio-epathology/
>>>
>>>
>>>
>>>
>>> On 4/7/2015 11:59 AM, Michael Giacomelli wrote:
>>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> Post images on http://www.imgur.com and include the link in your posting.
>>> *****
>>>
>>> I wonder if anyone has tried color calibrating a histology slide
>>> scanner?  I know they make kits for photography film scanners, but I'm
>>> not sure if that would work here.  Measuring the transfer function
>>> from the scanner and mapping onto sRGB would be the safest way to
>>> proceed I think.
>>>
>>> Mike
>>>
>>> On Tue, Apr 7, 2015 at 10:45 AM, Michael Giacomelli <[hidden email]> wrote:
>>>
>>>
>>> Hi Brian,
>>>
>>> I'm a little surprised that this is an issue, but I think you may be
>>> right.  Adjusting the gamma by approximately that amount makes the
>>> images look better. I'm not certain they're correct, but its certainly
>>> much better.
>>>
>>> A question though:  why is this even a problem?  As I understand it,
>>> the Aperio format includes color calibration information from the
>>> scanner (theres an option to apply it in their software), and it will
>>> take the color calibration from my monitor in Windows.  So it knows
>>> the gamma of both the display and scanner.  Why does it still end up
>>> wrong?  Is this a bug in Leica's software or do I not understand
>>> something?
>>>
>>> As an aside, I googled this imaging core and Aperio, and it brings up
>>> a lot of papers with badly oversaturated slides, so I'm pretty sure
>>> this isn't just me.
>>>
>>> Mike
>>>
>>> On Mon, Apr 6, 2015 at 7:18 PM, Armstrong, Brian <[hidden email]> wrote:
>>>
>>>
>>> Hello Mike, I believe that some scanners use a default gamma setting of 0.45
>>> for BF imaging. If this is the case then with the gamma at 1.0 it will
>>> appear oversaturated. Take a look at your gamma settings on Aperio Image
>>> Scope and see where it is set. Try the gamma at 0.45 and see how it looks.
>>> Ask your imaging partner what the gamma setting is on the Aperio scanner.
>>>
>>> Cheers,
>>>
>>> Brian Armstrong PhD
>>> Director, Light Microscopy Core
>>> Beckman  Research Institute
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Confocal Microscopy List [mailto:[hidden email]] On
>>> Behalf Of Michael Giacomelli
>>> Sent: Monday, April 06, 2015 4:02 PM
>>> To: [hidden email]
>>> Subject: Leica slide scanner calibration
>>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> Post images on http://www.imgur.com and include the link in your posting.
>>> *****
>>>
>>> I had some pathology slides scanned at a local imaging core on an Aperio
>>> scanner, but the color appears to be quite off.  Using the built in
>>> correction in the aperio visualization software (which I believe uses the
>>> correction information from the scanner), my H&E slides are kind of a hot,
>>> oversaturated pink.  Disabling it brings it closer to reality, but its still
>>> much too saturated.  Just to convince myself, I looked side by side between
>>> the scanned images and the original slides and used a second monitor.
>>> Something is wrong.
>>>
>>> I don't think this is my monitor, its an 8 bit IPS panel thats been color
>>> calibrated to ~100% sRGB using an X-Rite.  Besides giving excellent accuracy
>>> in the X-Rite measurements, other images look fine.
>>>
>>> My assumption is that it has to be the scanner itself.  Has anyone had this
>>> problem before?  I'm going to go back to the imaging core and try to talk to
>>> them about it, but I was hoping to find out a little bit more about the
>>> problem so I don't sound clueless when I say that my images look 'funny'.
>>>
>>> Mike
>>>
>>>
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>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>>
>>>
>>>
>>> George McNamara, Ph.D.
>>> Single Cells Analyst
>>> L.J.N. Cooper Lab
>>> University of Texas M.D. Anderson Cancer Center
>>> Houston, TX 77054
>>> Tattletales http://works.bepress.com/gmcnamara/42

[Grace Chojnowski-2]

Applications are invited for a full-time Flow Cytometry Analyst position to join our dynamic team in the Flow Cytometry and Imaging Core Facility at the QIMR Berghofer Medical Research Institute. Reporting to the Flow Cytometry and Imaging Facility Manager, the primary responsibilities of this position included, but not limited to assisting in the operation of multiparameter flow cytometers, high speed cell sorters, data acquisition and analysis. In addition, the applicant will also be required to assist the QIMR Berghofer microscopy staff with microscopy and imaging activities within the facility.  

QIMR Berghofer employs a critical mass of world-class researchers with over 50 research laboratories. The core facility is housed in new state of the art research facilities, comprising of six flow cytometry analysers and four cell sorters.  With the generous support from the ACRF, the facility is currently undergoing significant expansion and will house various confocal, multiphoton, intravital, spinning disk and deconvolution microscopes.

The applicant must have a minimum of a BSc or equivalent, flow cytometry and microscopy experience is desirable but not essential.  Staff members will have the opportunity for ongoing training and career development. The Ideal candidate will have the ability to work independently, have good verbal communication skills and are able to interact effectively with a broad range of individuals within the institute.  The position would suit an individual who has an aptitude and passion for working with complex instrumentation.

For further information please contact Email: [hidden email]  or phone [phone].

For a position description and to Apply  please go to  http://www.qimrberghofer.edu.au/page/Careers/Positions_vacant/ 

Reference 11994

 Kind Regards,
Grace
Please support my Ride to conquer cancer

Grace Chojnowski  |  Flow Cytometry and Imaging Facility Manager
QIMR Berghofer Medical Research Institute
 
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