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ome / ngff

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
https://ngff.openmicroscopy.org
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Add bia ngff link to data page #256

Closed will-moore closed 4 days ago

will-moore commented 3 months ago

Add link https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/idr_ngff_data.html to data page. NB data size is approx estimate from totals listed on studies.txt page before conversion to NGFF.

NB: I wonder if we want to add a note somewhere that opening Plates in vizarr often doesn't work because of the trailing /0 as it's expecting bioformats2raw format. E.g https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/S-BIAD847/02fb729e-803a-4c2e-b40c-cf58d839567c.html shows nothing, and when you open in vizarr you get: https://hms-dbmi.github.io/vizarr/?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD847/02fb729e-803a-4c2e-b40c-cf58d839567c/02fb729e-803a-4c2e-b40c-cf58d839567c.zarr/0 which looks broken. You need to remove the trailing /0 before it's viewable:

github-actions[bot] commented 3 months ago

Automated Review URLs

joshmoore commented 3 months ago

NB: I wonder if we want to add a note somewhere that opening Plates in vizarr often doesn't work because of the trailing /0 as it's expecting bioformats2raw format.

The other option, @will-moore, would be to update the pages themselves? cc: @matthewh-ebi

@manzt: any other ideas?

joshmoore commented 4 days ago

Filed https://github.com/ome/ngff/issues/274 as a follow-up