WSIs appear dark black when I convert SVS files to 10x or lower scale factor

[monjoybme]

Operating system

Linux

Platform

x86_64

OpenSlide Python version

1.1.2

OpenSlide version

3.4.1

Slide format

SVS

Issue details

Hi,

Some sections of the WSIs appear dark black when I convert SVS files to 10x or lower scale factor (some times even 20x or more) images [see attached sample]. I am not experiencing this issue with all images, but I believe it occurs when the SVS image size is large. When I increase the scale factor, I have no problems. Do you have any solutions for this?

[bgilbert]

This is probably https://github.com/openslide/openslide/issues/278. What Linux distribution and version are you using?

[monjoybme]

@bgilbert I am using Centos 7, Architecture: x86_64, CPU op-mode(s):32-bit, 64-bit. I installed conda install pixman=0.36.0, but the issue doesn't solve.

[bgilbert]

I don't know Conda. Is it possible that 0.38.0 is installed in parallel, and is still being used? I'd recommend making sure that 0.38 is uninstalled. The copy shipped natively in CentOS 7 doesn't have this issue, so the Conda copy is likely the problem.

[monjoybme]

@bgilbert This is not clear to me if pixman part of Centos or OpenSlide. I also tired the approach mentioned here , but it didn't work.

[monjoybme]

@bgilbert This is not clear to me if pixman part of Centos or OpenSlide. I also tired the approach mentioned here , but it didn't work.

Got it! It is a part ofOpenslide. Now installing Openslide from the beginning. Now I havepixman-0.40.0. Keep you posted. Thanks!

[monjoybme]

@bgilbert My problem has been resolved. I established a fresh conda environment and installed the most recent version of Openslide-python. I checked the pixman version, which was 0.40.0, during the Openslide installation. Pixman did not work when I installed it individually. Hence, a fresh installation of OpenSlide is advised. Thanks a lot for your help and guidance!