spatialdata
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An open and interoperable data framework for spatial omics data
Late followup PR of spatialdata from this: https://github.com/ome/ome-zarr-py/pull/261 also should point out that this is current only in the latest spec, not v0.4: https://github.com/ome/ngff/pull/202
Hi, Thank you for the help with the polygons previously. We're trying to investigate some polygons of interest but we get different cells selected when we investigate the same regions...
The `z` dimension in `shapely` objects can create problems downstream, as for example here: https://github.com/scverse/spatialdata-plot/issues/230. We should validate this at the level of the data model.
# TLDR; When #398 is addressed, we can remove `_check_element_not_on_disk_with_different_type()` as it will not be needed anymore. # Full issue When adding an element in-memory to a SpatialData object, the...
This is to collect points to discuss in major redesign of how IO interacts with the capabilities of extending an object by adding/removing or modifying particular elements. In other words,...
While writing tests for the incremental IO of metadata I added tests also for those metadata that we originally planned in the design doc for points but that we have...
The modular saving of elements and transformations has been refactored out of the previous release but it didn't make yet in the new codebase. Re-enabling this is a high priority.
When the `AnnData` object has obs that are not unique the join will fail because code like this `table[joined_indices, :]` require unique indices. I think we should - [ ]...
This works: ```python import zarr import spatialdata as sd root = zarr.open( "s3://bucket_name/spatial-sandbox/visium_associated_xenium_io.zarr", storage_options={ "endpoint_url": "https://objectstor.vib.be", }, ) sdata = sd.SpatialData.read(root) # sdata has content ``` This does not work:...
With `dask-exprs` landed, we need to adjust the code base for compatibility. Until we are compatible the version of dask used is constrained to a specific version.
