Data loaders for SpatialData elements

[keller-mark]

User story

Tasks

Beta Give feedback

1. Shapes - circles (with fixed radius)
2. Shapes - circles with radius column
3. Shapes - polygons
4. Points
5. Tables - single
6. Tables - multiple
7. Images
8. Labels

Old issue contents

See

• https://forum.image.sc/t/proposal-for-ome-ngff-table-specification/68908
• https://github.com/kevinyamauchi/ome-ngff-tables-prototype
• Table spec proposal ome/ngff#64

Preferred solution

• Implement a convenience file type table.ome-zarr which transforms a file definition that points to a Zarr store containing an OME-NGFF table prototype into minimal AnnData file types implemented in File types and data types to support obs-x-feature use cases #1261 (and image.ome-zarr or obsSegmentations.ome-zarr file definitions)
  • Options for obsLocations: { path } and obsSegmentations: { path } to support PointTables and RegionTables
  • Eventually options for Regions of Interest as discussed in Regions of Interest #1284

Remaining tasks after #1693

Tasks

Beta Give feedback

1. filtering by region (in multi-region tables)
2. Joint file type for spatialData
3. obsLocations for segmentation (labels / polygon) centroids - see note https://spatialdata.scverse.org/en/latest/design_doc.html#shapes ("the centroids coordinates can still be stored in obsm["spatial"] of slot of the Table, yet no coordinates system is defined for them. The assumption is that the coordinate system of the centroids corresponds to the implicit coordinates system of the Labels image")
4. obsPoints (point elements)
5. Coordinate transformations for spots? or are these coordinates always aligned to the post-transformation image?
6. Coordinate transformations for points? or are these coordinates always aligned to the post-transformation image?
7. ensure that the scale bar is implemented correctly - see Adding a pixel size in OMERO metadata scverse/spatialdata#357
8. non-power-of-2 scaling of multi-resolution images? - see a related discussion on DeckGL slack https://deckgl.slack.com/archives/C34AC5MSQ/p1697567517701879
9. Use the radius column of the shapes table

[will-moore]

I was just starting to look into vitessce's support for OME-NGFF and AnnData, hoping to view the proposed (soon to be merged?) NGFF table spec data in Vitessce. E.g. using sample data from https://github.com/kevinyamauchi/ome-ngff-tables-prototype/blob/main/examples/save_load_squidpy_segment.py as it appears in napari: ome/ngff#64 (comment)

I found this issue when trying to take the first step of viewing an OME-NGFF image in vitessce...

http://vitessce.io/docs/data-file-types/#rasterome-zarr

Using a config (below) based on the example there, and serving that locally: http://vitessce.io/#?edit=false&url=http://localhost:8000/vitessce/image_config.json I got:
"The dataset configuration is missing a version, preventing validation."

{
  "url": "http://localhost:8000/6001247.zarr",
  "type": "raster",
  "fileType": "raster.ome-zarr"
}

I don't see a version on any other examples on that page, so not sure what to use.

I see that the docs at https://github.com/vitessce/vitessce/blob/main/docs/docs/data-file-types.mdx#imageome-zarr are quite a bit different from those deployed above, so I'm not sure which to use for the app at http://vitessce.io?

[will-moore]

Ah - with #1167 I found the example at https://github.com/vitessce/vitessce/blob/main/src/demo/view-configs/blin.js to be helpful

[keller-mark]

https://spatialdata.scverse.org/en/latest/tutorials/notebooks_repo/datasets/README.html

https://github.com/scverse/spatialdata-notebooks/tree/main/datasets

[keller-mark]

https://github.com/scverse/spatialdata-notebooks/tree/dev_notebooks/notebooks/developers_resources/storage_format

[keller-mark]

ome/ngff#138

[keller-mark]

https://kylebarron.dev/parquet-wasm/