spatialdata
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scverse
An open and interoperable data framework for spatial omics data
Sometimes (I can't reproduce consistently, it happens rarely), the tests for `deepcopy()` fail because the deepcopied points have columns with shuffled order. See for instance here: https://github.com/scverse/spatialdata/actions/runs/8281155947/job/22659046336?pr=455 I can't reproduce....
This is to keep track of issues that might arise on the relationship between `instance_key` and the indexes of regions. ### Motivation The link between a table and it's region...
As reported here, https://github.com/scverse/spatialdata-io/issues/117 querying a raster element and trying to save it may lead to the following error: ``` ValueError: Attempt to save array to zarr with irregular chunking,...
Gitpod
This PR adds a config file for gitpod, which will allow to start a Gitpod instance from the spatialdata container. Currently, this is pointing to a test placeholder container I...
I discussed this with @melonora today. Relevant also to @timtreis and @sagar87. CC @giovp I would add a method to check the consistency of the table and the elements. This...
When rasterizing images or labels (basically resampling), there is an offset (see picture) that I think is due to the fact that somewhere in the code for rasterization the coordinates...
For example, I can't figure out how to use segmentation algorithms with squidpy with the images stored in the spatial data. I know I can load these images in straight...
tl;dr: Observation windows are a crucial piece of spatial metadata. It should be possible to associate `SpatialData` objects and elements with observation windows. Polygon elements can describe observation windows, but...
If something goes wrong while writing a component of a Zarr store, especially a .zattrs (JSON) file, then the corrupted data could prevent the Zarr store to be read. We...