Strange .svs import problem

Hello, lately I’ve been performing maintenance on some older legacy code and there is a certain problem that i can’t seem to figure out, We’ve been using loci-tools to open .svs images via ImportProcess, and for certain images it behaves very strange.

At scaled down resolution the images looks correct, but opened at full resolution the background coloring seems to vary wildly, I’ve attached code and how it currently looks. I am honestly completely dumbfounded. You can see how one image at full resolution looks good, but the other has a strange pink shade all over it.

When the images are opened in ImageJ with the Bio-formats plugin it works correctly and as intended, so are there perhaps better ways code-wise to do open these images that I’m missing? I’m still learning how to work with ImageJ so forgive me if this is a stupid question.

Image of ROI:s at lower resolution:

Image of ROI:s at full resolution (notice the strange pink shade on image #1:

The code in question (you can safely ignore most of the parts relevant to the crop):

Since this is a Bio-Formats issue, I suggest you ask this question through the OME support channels. See also the Bio-Formats Reporting a bug page.

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Alright I’ll post it over there, thanks!


If anyone is wondering, I found the problem and it had to do with the auto scale - option. Adding options.setAutoscale(false); fixed it.