spatialdata
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scverse
An open and interoperable data framework for spatial omics data
I wonder if it's possible to support sparse array to some degree in Labels. If it's a mask then the sparse format could save quite a lot of disk space....
Parsing dataframes with zero length may lead to subtle bugs and has probably no use case. An example is to `to_zarr.py` script for the `cosmx_io` data in the sandbox. Parsing...
Right now in the schema we don't check if a `GeoDataFrame` shapes object contains mixed types. I would allow only the following two cases: - [ ] The geometry column...
replaces #565 #622 iteration over 20 batches, single worker new implementation main one annoying thing is that the "apply" method of the dataframe to get the bounding box selection is...
We should make the usage of datasets more heterogenous across the notebooks in the docs. Practically: - [ ] select 1, max 3, small datasets (
`spatialdata` is currently not available in `conda-forge` because [`xarray-dataclasses-feedstock`](https://github.com/conda-forge/xarray-dataclasses-feedstock) was not up-to-date (`xarray-dataclasses` is one of dependencies upstream). Now thanks to @jdblischak and @giovp the blocker is removed 🥳 Thanks!...
Draft PR so we can keep track of progress during the hackathon. These changes would need to land on main, so we can start with the API refactor Include: #905...
When concatenating sdatas, the function doesn't touch the coordinate systems. This can lead to coordinate systems that accidentally having the same name (f.e. `global`) suddenly having elements that shouldn't be...
In `_vectorize_mask`, we pad the mask before using `find_contours`, which is needed to have correct geometries. Yet, it create a shift of one pixel in the coordinates. This PR shifts...
There is a minor issue in `spatialdata._core.operations.vectorize._vectorize_mask` The interior is removed when we have a mask with an interior, for instance this one: ```python import numpy as np mask =...