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imi-bigpicture / wsidicomizer

Python library for converting WSI files to DICOM
Apache License 2.0
54 stars 7 forks source link

Remove OpenSlide as a dependency #60

Closed sarthakpati closed 1 year ago

sarthakpati commented 1 year ago 
          I would also add that openslide is not particularly important/useful for pythonic environments. It would be better to use something like tiffslide in its stead.

Originally posted by @sarthakpati in https://github.com/imi-bigpicture/wsidicomizer/issues/7#issuecomment-1479604857

erikogabrielsson commented 1 year ago

For now openslide is needed to support mirax files. Tiffslide has a work in progress to support mirax, but until it does openslide should be kept.

However, adding support for reading from tiffslide might be worth implementing earlier, as for example the fsspec support. Im currently refactoring how wsis are opened (starting in wsidicom), but can do a simple implementation after that.

sarthakpati commented 1 year ago

Awesome! It would be great if you could at least put openslide import as a try-except for files that tiffslide does not currently support. This would not break the functionality of wsidicomizer, as well as ensure that when tiffslide's file support increases, it would be trivial to remove the openslide components. What do you think?

erikogabrielsson commented 1 year ago

Yes openslide will be moved to an extra-category.

erikogabrielsson commented 1 year ago

Closed with #63