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qupath / qubalab

Lab for quantitative bioimage analysis experiments in Python
Apache License 2.0
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OpenSlide and TiffSlide #18

Closed alanocallaghan closed 1 week ago

alanocallaghan commented 2 weeks ago

Spotted in #16, #15 and #14...

In the current tests, we write pyramidal RGB tiffs:

https://github.com/qupath/qubalab/blob/13a9f0f3ad3d9bf088027e40d3c30e0b8d1a6970/tests/res/multi_resolution_uint8_3channels.py#L76-L85

When photometric='rgb', OpenSlide works fine. TiffSlide fails with NotImplementedError: series with axes='SYX' not supported yet. Without setting this flag, TiffSlide "works", but returns all zeros for all pixels. OpenSlide fails with openslide.lowlevel.OpenSlideUnsupportedFormatError: Unsupported or missing image file.

An unrelated issue with OpenSlide on Linux was resolved in #14, where the apt version of OpenSlide fails to read the pixel calibration from the image properties. Theoretically we could parse this from the image metadata ourselves, but it's probably more prudent to wait for 4.0.0 binaries to be out on apt (and linked up with python).

Now reading the openslide-python README might make you think that you can pip install openslide-python openslide-bin and get a working openslide install. But we have to wait for openslide-python 1.4.0 for that! Given openslide-bin was released 3 weeks ago, that should be soonish

https://github.com/openslide/openslide-python/blob/797ea3ddb981713ba0b07a91d79f9396338dda9b/README.md?plain=1#L49-L56

alanocallaghan commented 1 week ago

Leaving tiffslide in place just in case