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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 <[log in to unmask]> 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
> <[log in to unmask]> 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 <[log in to unmask]> 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 <[log in to unmask]> 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:[log in to unmask]] On
>> Behalf Of Michael Giacomelli
>> Sent: Monday, April 06, 2015 4:02 PM
>> To: [log in to unmask]
>> 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