Tables - Githubissues

will-moore commented 1 year ago

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 and obsm 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 with dtype: <i8, which means data such as obs/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

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