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 @leandervaneekelen, any updates on my previous message? thanks! |
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* Add omezarr package requirements * Init OMEZarr reader * Add OMEZarr reader support based on changes in #163 * Fix OMEZarr thumbnail algorithm and correct init flag to updated variable name * Update pyproject.toml Change the ome-zarr dependencies to hopefully work better with the strict package requirements of aicsimageio. * Update omezarr reader to successfully run through the same commands in test_openslidewsi.py * Add further OMEZarr reader references didn't change index.rst as the support is probably more narrow than any conception of a WSI in the zarr format. * Change OMEZarr WSI properties to dictionary * Change OMEZarrWSI documentation slightly * Update comment for OMEZarrWSI property dictionary * Fix py310 environment * Move OMEZarr support to be optional * Update OMEZarrWSI.py following PR review Fix assumption that ngff-multiscales have a strict dimension ordering Format code with black and autopep8 Move imports that are now optional to a try except block Add docstring to _fetch_downsamples Optimise read_region by adding some processing to lazy_initialize * Fix OMEZarr robustness issues Make imports more robust Expand possible dimnames Fix incorrect OME spec assumption in fetch_mpp Update slice varname for better readability Cache slice involved variables in init rather than read * Update docs for optional install * fix: naming in progress bar --------- Co-authored-by: Harvey South <harveysouth@hotmail.co.uk> Co-authored-by: Harvey South <73258129+HarveySouth@users.noreply.github.com>
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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.