galaxyproject / galaxyproject/galaxy

[WIP] Image file format support

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#7,066 2 comments 1 reaction 0 assignees View on GitHub
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Python
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Description

My wishlist of image formats that are heavily used in life sciences and should be supported by Galaxy:
- [ ] DICOM #18895
- [x] NIfTI https://github.com/galaxyproject/galaxy/pull/11020
- [x] ome-tiff https://github.com/galaxyproject/galaxy/pull/11801
- [ ] TIFF(pyramidal tiled TIFF, BigTIFF) with endings .svs, .tif, ...
- [ ] Bioformats https://docs.openmicroscopy.org/bio-formats/5.9.2/supported-formats.html

Can't we just check for most of them by file signature like https://en.wikipedia.org/wiki/List_of_file_signatures

Contributor guide

Open the contributing guide

Research direction

Start by reviewing the remaining checklist in this issue and the referenced pull requests, especially #18895, #11020, and #11801, to understand Galaxy's existing image-format support. Define the scope for the uncompleted formats and file-signature detection, then confirm that each selected format is recognized and usable in Galaxy.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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