http://confocal-microscopy-list.275.s1.nabble.com/Leica-slide-scanner-calibration-tp7583619p7583672.html
> 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