Implement DICOM image reader #163
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| self.job_dir = job_dir | ||
| self.wsi_source = wsi_source | ||
| # TODO: should I add DICOM here as well? |
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yes, we can include dicom here too.
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Hi @leandervaneekelen, thx for the PR! I thought openslide was supporting DICOM (https://forum.image.sc/t/openslide-4-0-0-released/87323)? Or only some of the DICOM slides? Can you shared a DICOM slide so i can test on my end. thx |
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Hi Guillaume and co,
I frequently work with WSIs scanned as DICOMs. This PR implements support for this format by wrapping a reader around wsidicom in a similar way to #150 which was written for SPDC.
One caveat is that DICOMs break away from the typical "monolithic" file format such as a
.tifor a.svsfile, instead opting for being contained in a folder with an arbitrary amount of.dcmfiles. This necessitates the existence of a small util function_is_dicom_folder. This doesn't fit the typical design pattern of checking the extension of a file to determine its file type, and I was unsure whether or not you'd like a bigillion_is_dicom_foldercalls incollect_valid_slidesfor batched processing. Let me know what you think.