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ome / ome-ngff-tools

Document available viewers and other tools for the OME-NGFF image format
https://ome.github.io/ome-ngff-tools
BSD 3-Clause "New" or "Revised" License
2 stars 4 forks source link

Add Allen Institute’s Cell Feature Explorer #21

Open will-moore opened 1 year ago

will-moore commented 1 year ago

Mentioned at https://forum.image.sc/t/fast-online-stack-browser/74691/23

E.g. with the link from post above: https://allen-cell-animated.github.io/website-3d-cell-viewer/?url=https://animatedcell-test-data.s3.us-west-2.amazonaws.com/variance/1.zarr

or with IDR example https://allen-cell-animated.github.io/website-3d-cell-viewer/?url=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457537.zarr

NB: It seems that the viewer only works with 5D data - E.g. https://allen-cell-animated.github.io/website-3d-cell-viewer/?url=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr fails with 

Uncaught (in promise) RangeError: too many indices for array; expected 4, got 5
    at checkSelectionLength (core.mjs?3f36:250:1)
    at replaceEllipsis (core.mjs?3f36:334:1)
    at normalizeArraySelection (core.mjs?3f36:277:1)
    at new BasicIndexer (core.mjs?3f36:412:1)
    at ZarrArray.getBasicSelectionND (core.mjs?3f36:2715:1)
    at ZarrArray.getBasicSelection (core.mjs?3f36:2711:1)
    at ZarrArray.get (core.mjs?3f36:2696:1)
    at eval (FetchZarrWorker.js?ed40:65:1)
imagesc-bot commented 1 year ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/fast-online-stack-browser/74691/24

toloudis commented 1 year ago

As of today it expects TCZYX but accepting CZYX or TZYX should be an easy enough change. I'll probably add that very soon to make that test data work.

toloudis commented 1 year ago

Also FYI regarding naming: Cell Feature Explorer is the dataset presentation app at https://cfe.allencell.org and the 3D viewer component is a part of it which we called website-3d-cell-viewer but haven't bothered to rename since we started to make it something that could stand alone. It is in need of new naming since now it can behave as a standalone viewer and also has been embedded into jupyter notebooks as nbvv