spatialdata-io
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---Hello, I am currently encountering the following issue: a problem with reading Cosmx. It was installed through the following method: conda create -n spatial-data python=3.11 # python >= 3.11 pip...
Since the release of `pyarrow 22.0.0` the CI started failing, with errors similar to the one below. Please note that the error doesn't seem to be `spatialdata`-related. [Full CI run...
Hi, I am using spatialdata-io v0.3.0 and trying to read the data from the Xenium bundle with this command xenium_bundle_path = "/path/to/xenium/data" zarr_path = "/path/to/workdir" sdata = xenium(xenium_bundle_path) but I...
See suggestions from @ckmah in Zulip: [#spatialdata-dev > unifying readers @ 💬](https://scverse.zulipchat.com/#narrow/channel/443514-spatialdata-dev/topic/unifying.20readers/near/548248316).
This is the cosmx reader from Sopa, which includes: - stitching - FOV shift correction (for a specific buggy version of AtomX) - support for the Protein Assay - handle...
Hello @timtreis and @LucaMarconato, As discussed yesterday, I'm starting to move some readers from Sopa. See the [original issue in Sopa](https://github.com/gustaveroussy/sopa/issues/240) where we discussed the reader creation. It appears that...
Towards #228 Replace the code to load the Xenium segmentation masks to use Dask to greatly reduce the memory consumption of the Xenium reader. I abandoned the idea of saving...
What kind of feature would you like to request? Additional function parameters / changed functionality / changed defaults? Please describe your wishes will scanpy add support for this thanks a...
Convert to RGB format so that colors will display correctly as RGB in napari-spatialdata.
