http://confocal-microscopy-list.275.s1.nabble.com/Leica-slide-scanner-calibration-tp7583619p7583639.html
access to and our core facility's Aperio to Leica. Their initial
from an engineer there. Hopefully this is something that can be
calibrated. I expected them to use reference slides, much like you
would calibrate a digital camera. Its a little troubling to me that
> 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