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PathologyDataScience / HistomicsML2

A tool for training machine-learning models with whole-slide imaging datasets
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WSI files formats #63

Closed Reasat closed 3 years ago

Reasat commented 3 years ago

The tutorials focus on transforming .svs files to tif. Are other files supported? For example .scn from leica scanners? https://openslide.org/formats/leica/

Which part of the code should I modify to support .scn files?

slee172 commented 3 years ago

@Reasat HistomicsML2 uses the IIP image server(https://iipimage.sourceforge.io/documentation/server/) to display multi-resolution TIFF formatted images. The SVS images can be converted to the TIFF by using a bash shell script. You can find the bash shell script(create_tiff.sh) from here (https://histomicsml2.readthedocs.io/en/latest/data-create.html#download-the-dataset-creation-container). The 'create_tiff.sh' contains libvips in the code. So, you can test it following here https://libvips.github.io/libvips/