I have just installed Cytomine on a server following the tutorial. Although I am able to upload and browse images from scanner vendors with no problem (I’ve tried MRXS from 3DHistech), I am experiencing visualization issues with custom TIF files.
We are not allowed to use “raw” files from the scanners due to privacy concerns. Therefore, we first convert the slide by reading the entire image on a patch-by-patch basis and writing the tiles to a regular TIF. This way, we convert any image format to an anonymous TIF file.
Although I can browse these TIF files with other tools (e.g. GitHub - computationalpathologygroup/ASAP: Program for the analysis and visualization of whole-slide images in digital pathology), I see image artifacts when they are uploaded to Cytomine. I’ve attached some pictures of these artifacts for two different TIF files.
Do you recognize these artifacts or have any clue what the problem could be? Alternatively, where can I find logs that could help me debug the issue?