spatialdata
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scverse
An open and interoperable data framework for spatial omics data
Fixes https://github.com/scverse/spatialdata/issues/799 The [to_parquet](https://geopandas.org/en/stable/docs/reference/api/geopandas.GeoDataFrame.to_parquet.html) function supports a `geometry_encoding` parameter. When [geoarrow](https://geoarrow.org/), it will be more efficient to read/parse the geometries, as the data can stay in its parquet/arrow memory layout...
When constructing an Image2DModel, the following code will work: ``` from multiscale_spatial_image.to_multiscale.to_multiscale import Methods sdata.images['my_image'] = sd.models.Image2DModel.parse( imarr, dims=['c','y','x'], c_coords=['DAPI','ATP1A1/CD45/E-Cadherin','18S','alphaSMA/Vimentin'], scale_factors=[2,2,2,2,2,2,2,2], method=Methods.XARRAY_COARSEN, chunks=(1,256,256), ) ``` However, the following code will...
This PR clarifies how to access the attributes listed here when accessing the points data from the on-disk format. Is this correct that the coordinate transformations are in `"transform"` in-memory...
Hi, I wanted to clarify the logic for inferring the intrinsic coordinate system name here by adding an example. Please let me know if this understanding of how the intrinsic...
The `spatial_data.read_zarr` function raises an error when trying to read a `Group` from `zarr` version `2.18.7` as it tries to turn the `Group` into a `Path` object directly when `Group`...
https://github.com/scverse/spatialdata/blob/8c3e51880004499304f79b17e3b36d2fb5e9dd82/src/spatialdata/_core/query/relational_query.py#L530-L534 > …/spatialdata/_core/query/relational_query.py:530: FutureWarning: functools.partial will be a method descriptor in future Python versions; wrap it in enum.member() if you want to preserve the old behavior you should test with...
The code print(sdata) print(sdata.tables['table']) def crop(sdata): return sdata.query.bounding_box( min_coordinate=[2000, 2000], max_coordinate=[2200, 2200], axes=("x", "y"), target_coordinate_system="global" ) print() csdata=crop(sdata) print(csdata) does not return any error, but the cropped csdata does not...
**Is your feature request related to a problem? Please describe.** I am working with two images from adjacent slices of the same tissue: a fluorescence image and an H&E image....
In Bioconductor, packages are tested against first-order dependents. We should consider doing this, as done for `scverse` packages depending on `AnnData`: https://github.com/scverse/integration-testing/actions/runs/18115461787. In this way we can flag installation incompatibilities...
Hi, I'd like to first start this conversation then create more specific issues in points you agree with me. I have some suggestions about modifying and generalizing the internals of...
