spatialdata
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An open and interoperable data framework for spatial omics data
All tests pass with `dask==2024.11.2`. With `dask==2024.12.0` and `dask==2024.12.1` the following 10 tests fail:  More recent versions of `dask` (from `2025.1.0` onwards), cannot be installed at the moment due...
Whole slide image (WSI) data plays a significant role in the digital pathology field. However, integrating WSI into SpatialData is quite challenging. What makes WSI different: 1. **Large file size**:...
Originally reported by @Felicie-Giraud-Sauveur via [Zulip](https://scverse.zulipchat.com/#narrow/channel/315824-spatial/topic/Opening.20sdata.20with.20a.20more.20precise.20selection/near/496543171) > I currently use sdata = sd.read_zarr(f"path/sdata.zarr", selection=("tables",)) to open only the tables for example. But now I am starting to have a large...
Originally observed by @ilia-kats When constructing a `ImageTileDataset` without using rasterization, a shape mismatch bug could occur (the returned tiles are not all of of the same size). This bug...
Running this code with Python 3.11 shows ```python from spatialdata._core.query.relational_query import JoinTypes; print(JoinTypes._member_names_) from spatialdata._core.query.relational_query import MatchTypes; print(MatchTypes._member_names_) ``` ``` ['left', 'left_exclusive', 'inner', 'right', 'right_exclusive'] ['left', 'right', 'no'] ``` While...
The 4 subclasses of `RasterModel.parse()` 2D/3D images/labels, accept `DataArray` as arguments, but do not accept `DataTree`. For consistency we should add this option. Until this is added, the recommended usage...
The `xarray.DataArray` constructed here https://github.com/single-cell-data/TileDB-SOMA/blob/fe8e64d88173b0d79d93893a778eb481a75ff2c5/apis/python/src/tiledbsoma/io/spatial/outgest.py#L309 creates a object that passes our validation but that differs from the same object after a call of the parser in the `.indices` and `.coords`....
Hi! Thanks for the great package! I am currently working with `spatialdata` to load and parse microscopy files (particularly in the proprietary Carl Zeiss `.czi` format). For this purpose, it...
We have a single `read()` function that is internally reading the single elements one by one as private functions. We need to expose public APIs for incremental reading, as we...
NOTE: This can be easily solved by updating to v0.2.7-pre0, but I thought I would notify of the breaking change anyways. Within the past hour of me posting this, the...
