spatialdata
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An open and interoperable data framework for spatial omics data
New design discussed here: https://hackmd.io/EKGHONTUS4usTOEsj4k3oQ
We should make small datasets with all elements represented available for interoperability testing (e.g., can all elements be loaded into R or Vitessce)
When transforming a MultiscaleSpatialImage, a KeyError is raised. See https://github.com/scverse/spatialdata/issues/378 So far, I've modified the test case to cover both SpatialImage and MultiscaleSpatialImage and reproduce the problem. I have no...
Hi, I'm trying to create a spatialdata object of a MERSCOPE experiment from the vpt output file but there is an index mismatch error when generating the anndata file Here...
When type-hinting my code, I frequently need `Sequence` from `collections.abc`. In order to avoid name clashes, one can do for either of the two: ```python from spatialdata.transformations import Sequence as...
When running the vignette [Use landmark annotations to align multiple -omics layers](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/alignment_using_landmarks.html), I run into an attribute error on cell #2 ``` xenium_sdata = sd.read_zarr("xenium.zarr") xenium_sdata ``` The error is...
Implement, and document in a notebook, an helper function for accessing levels of multiscale images
Asked by @berombau. One public function similar to this is here https://github.com/scverse/spatialdata/blob/4c6c1e9613310acc8844ff186a66084e8d5b85e4/src/spatialdata/_utils.py#L170. - [ ] We could make the function accept an int argument instead. - [ ] We definitely...
The [implementation of `transform`](https://github.com/scverse/spatialdata/blob/cf1c1f74c9aaa1f99eca3ebc363cc990e381fb7d/src/spatialdata/_core/operations/transform.py#L262C9-L262C10) for `MultiscaleSpatialImage` is not covered by tests. This is a problem because (Multiscale)SpatialImage are structurally and implementationwise significantly different. For scale1 and greater, the key is...