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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 <[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
>>
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>> 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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