spatialdata
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scverse
An open and interoperable data framework for spatial omics data
The skimage.segmentation.slic call segfaults occasionally on arm64 mac
Hello, thank you for providing the community with such a great tool! I was wondering if you could help or advise on the following. I have a very large xenium...
**Describe the bug** On a fresh spatiadata installation, running https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/technology_visium_hd.html fails at the "Plotting gene expression data" / "Plotting the vector geometries" step with: ``` --------------------------------------------------------------------------- ValueError Traceback (most recent...
As title, otherwise new features breaking main but not released lead to broken docs notebooks.
Originally reported by @ilan-gold [via Zulip](https://scverse.zulipchat.com/#narrow/channel/315824-spatial/topic/.60SpatialData.60.20Type.20documentation/near/501532935). > Hello! A very simple question/request - how would I find out what the type of Images is from the documentation https://spatialdata.scverse.org/en/stable/api/SpatialData.html#spatialdata.SpatialData.images xarray? dask?
I get an error when I load the example `.zarr` as a `SpatialData` object in [the tutorial](https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/intro.html). The link to the example dataset (https://s3.embl.de/spatialdata/spatialdata-sandbox/mouse_liver.zip) uses an unrecognized Version 0.6-dev. Here...
**Recommendation: attach a minimal working example** Generally, the easier it is for us to reproduce the issue, the faster we can work on it. It is not required, but if...
The daily CI failed on install for spatialdata failed. Please go to [the logs of the integration testing repo](https://github.com/scverse/integration-testing/actions/runs/13403296631) to review. @scverse/anndata
Local representation of the SpatialData object when read in locally. This is a Visium HD dataset that I created originally using `spatialdata_io.visium_hd` + some post-processing stuff. ``` SpatialData object, with...
