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hubmapconsortium / ingest-validation-tools

HuBMAP data submission guidelines, and tools which check that submissions adhere to those guidelines.
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Change af and stained directory schema: .tif and .tiff extensions should be allowed #710

Closed NHPatterson closed 3 years ago

NHPatterson commented 3 years ago
  • Does this change have buy-in from other groups providing the same kind of data?

Limited to ".tif" in the scheme is not correct. We are specifying that microscopy is packaged in OME-TIFF format which abbreviates Open Microscopy Environment - Tagged Image File Format. While ome.tif is current and acceptable, ome.tiff is should also be allowed as this is the default specification by bioformats, progenitors of OME-TIFF (see links below).

  • Can you quote or reference any outside documentation that motivates this change?

https://docs.openmicroscopy.org/bio-formats/6.6.1/formats/ome-tiff.html?highlight=ome%20tiff%20specification https://docs.openmicroscopy.org/ome-model/6.2.2/ome-tiff/specification.html

  • Is this change backward compatible, or does it make validation more stringent?

Yes it should be. A wildcard in the regex should allow both ome.tif and ome.tiff, or if only one is preferred, ome.tiff should be preferred.

@icaoberg will evaluate this request, and if it can move forward, will file a PR for @pdblood to review, and @mccalluc will make sure tests pass before merging.

one solution

https://github.com/hubmapconsortium/ingest-validation-tools/blob/b3c065b871c8f060ef7a7be27b3bb3bdae143260/src/ingest_validation_tools/directory-schemas/af.yaml#L12

-
  pattern: 'processedMicroscopy/[^/]+_preIMS_images/[^/]+\.ome\.tif*'
  description: 'OME TIFF files (multichannel, multi-layered, image pyramids) produced by the autofluorescence microscopy linked to IMS experiment'
icaoberg commented 3 years ago

@NHPatterson this issue has been addressed in branch icaoberg-vanderbilt-update cc @khanshawPSC