spatialdata
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scverse
An open and interoperable data framework for spatial omics data
Hi, This may be a question for SOPA but I thought it was also worth asking here as well please. I have custom polygon segmentation for a particular cell type...
The requirement pygeos fails to install with python 3.12 with the error described here: https://github.com/pygeos/pygeos/issues/463 The maintainer explains that pygeos is no longer maintained and has been merged into the...
Hi, I am wondering if it is possible to extract image features from a visium HD dataset using spatialdata and squidpy? Is this supported? Thanks, Sokratia
Closes #441, depends on (https://github.com/ome/ome-zarr-py/pull/349)
Hi @LucaMarconato ! I got an error when I use `aggregate()` to aggregate a label layer by a shape layer. Here is my code:    The label layer...
As pointed out here https://github.com/ckmah/bento-tools/pull/104#discussion_r1454146578, we should be able to drop the `pygeos` dependency. We need to try it out. Also this could be a solution to this behavior: https://github.com/scverse/spatialdata/issues/272.
I was testing the new mutlitple tables feature on the main branch, and noticed that automatic backing of sdata.tables to the backing zarr store no longer works (or I fail...
While I in the end was able to concatenate the data the way I like, the user experience wasn't as great as I had hoped, so wanted to drop some...
Right now, there is support for local .zarr stores and remote stores publically accessible via HTTP or S3. Private remote stores are more difficult, as they need certain options or...
Depends on #501. Prototype for backward compatible GeoParquet support for shapes, with ability to read/write data from/to the legacy format.