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choosehappy / HistoQC

HistoQC is an open-source quality control tool for digital pathology slides
BSD 3-Clause Clear License
265 stars 106 forks source link

Doesn't support TIFF? #159

Closed abhishekvahadane closed 4 years ago

abhishekvahadane commented 4 years ago

2020-03-18 10:41:48,544 - INFO - /S-190413-00241/vHnE/VHNE_S-190413-00241_R001.tif <class 'openslide.lowlevel.OpenSlideUnsupportedFormatError'> OpenSlide does not support the requested file. Import this from openslide rather than from openslide.lowlevel. ('Unsupported or missing image file', '/S-190413-00241/vHnE/VHNE_S-190413-00241_R001.tif', '<code object init at 0x10ba12930, file "/Users/abhishek.vahadane/DATA/RMI/code/HistoQC/BaseImage.py", line 44>')

choosehappy commented 4 years ago

Correct, HistoQC uses openslide which currently only supports whole slide image (WSI) formats.

Note, best practices states that quality control should be done on a WSI level and not as a cropped region of interest level