Leica SCN images with wrong colour

I have a large collection of SCN images and I intend to convert them to a non proprietary format for storage. These are general H&E files but they import onto imageJ with a pink background with a grey colour. I have tried various bio-format import options without success.
I can also comment that some other SCN files are importing correctly, so I am not sure what to do. Happy to share the images to support the import. Here I have two images from the same slide, one correctly imported and the other not…

Hi @Joao_Miguel, do you know what versions of Bio-Formats you are using? We have had fixes for similar issues in the past so it might be worth updating to 6.3.1 if you are not already using it.

If you are seeing the issues with the latest version then please submit a sample to https://www.openmicroscopy.org/qa2/qa/upload/

It was the 6.3.1 already as I just installed. I am submitting a sample of the images

Submitted two files, Oral_Biology_31.scn and Oral_Biology_33.scn. Both open without issues on the proprietary Leica SCN400 Image Viewer [1.4.13240]

Thanks @Joao_Miguel for providing the sample files. I was able to reproduce the issue with the latest Bio-Formats release and have opened a GitHub Issue to track the bug: https://github.com/ome/bioformats/issues/3510


Hi, has this issue been solved?

Im afraid this is still a known issue as we do not yet have a suitable fix for the bug.