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IDR / ome-ngff-samples

A catalog of all public OME-NGFF representative samples derived from IDR data
https://idr.github.io/ome-ngff-samples
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bioformats2raw.layout sample #15

Closed will-moore closed 1 year ago

will-moore commented 1 year ago

We currently have no bioformats2raw examples in this list. Prompted by https://forum.image.sc/t/intermission-ome-ngff-0-4-1-bioformats2raw-0-5-0-et-al/72214 I've started to add 1 with this PR...

This is v0.2 (which is currently the output from bioformats2raw). Since bioformats2raw.layout isn't supported by vizarr, I don't show the vizarr link if the Keywords column is bioformats2raw.layout

Can be viewed in ome-ngff-validator: https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.2/idr0070A/9838562.zarr

joshmoore commented 1 year ago

Good point. Or would it be cleaner to have everything go to the validator?

sbesson commented 1 year ago

@will-moore the following datasets:

are examples of OME-NGFF samples which use both the plate and the bioformats2raw.layout specifications

If we start registering the existence of the layout in the keywords column we can probably annotate these two rows as well.

In that case, vizarr will still be functional though as it will be able to interpret the plate metadata.

will-moore commented 1 year ago

@sbesson done