Closed will-moore closed 10 months ago
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This pull request has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/generating-vitessce-config-via-javascript-api/75678/1
This pull request has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/roi-annotations-and-tracking-information-in-ome-zarr/65975/4
Closing, since https://github.com/ome/ngff/pull/64 is closed.
Work in progress...
Starting to look at how to parse and display table data - see https://github.com/ome/ngff/pull/64/
Test: https://deploy-preview-20--ome-ngff-validator.netlify.app/?source=https://minio-dev.openmicroscopy.org/idr/temp_table/test_segment.zarr/tables/regions_table
Currently showing
X
,var
,obs
andobsm
data:Using sample data generated with https://github.com/kevinyamauchi/ome-ngff-tables-prototype/blob/main/examples/save_load_squidpy_segment.py with some tweaks at https://github.com/kevinyamauchi/ome-ngff-tables-prototype/pull/12
This data appears in napari like this (screenshot): https://github.com/ome/ngff/pull/64#issuecomment-1310600810
Initially, this shows a link when viewing the image that has a table. Clicking the link shows the full table page, coloured to match the AnnData scheme.
Limitations:
zarr.js
doesn't support data withdtype: <i8
, which means data such asobs/cell_id
needs to have dtype fixed (see PR above).The current implementation differs from the spec as described at https://github.com/ome/ngff/pull/64/files#r1022784696 with a single table at
test_segmetation.zarr/tables/region_table/.zattrs
(as generated by the script above).cc @kevinyamauchi