spatialdata
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scverse
An open and interoperable data framework for spatial omics data
## Bug description I recently stumbled upon a bug when trying to aggregate intensities on large multi-scale image elements. The bug occurs actually occurs in `spatialdata.transform`. ### Reproducer ```python import...
I work on a dataset with 1000 images and create and delete a lot of labels for these images. Writing and deleting label objects via write_element / delete_element_from_disk can take...
For many use cases (like xenium) points can be handled completley in memory without issue. Given that, and all the reasons the first "best practice" in the dask dataframes documentation...
Suggested by @vjcitn We could add some functions to help validation of disk data (e.g. to see if a Zarr store contains a valid `SpatialData` object, or if a particular...
I performed the installation using the following approach： ``` # Python==3.9.0 # spatialdata 0.2.5.post0 # spatialdata-io 0.1.5 # spatialdata-plot 0.2.7 pip install spatialdata pip install "spatialdata[extra]" ``` When running the...
Issue to keep track of this particular aggregation case. Currently when aggregating points by shapes, all the points are loaded into memory. Ideally this would be done incrementally by keeping...
When trying to get centroids of labels, the function `get_centroids` is really taking forever, even on small data. This makes it very difficult to run on real life data. For...
See context here: [#data-structures > JSON in `uns`](https://scverse.zulipchat.com/#narrow/channel/315789-data-structures/topic/JSON.20in.20.60uns.60/with/517500234). Status: - `.attrs` in `pandas` (hence in `geopandas` and `dask.dataframe`) are JSON-serializable, as [shown here](https://github.com/pandas-dev/pandas/issues/51012#issuecomment-1743856513). - In `SpatialData` we can enforce that....
Hi spatialdata team, Thank you for your work on this important project! We are currently generating multiple terabytes of multi-modal digital spatial transcriptomics data, including H&E images, gene expression, spatial...
### **Bug Description** Concatenating two `SpatialData` objects extracted from bounding boxes fails with a `ValidationError`. ### **To Reproduce** ```python import spatialdata as sd sdata = sd.datasets.blobs() sdata1 = sdata.query.bounding_box(('x', 'y'),...
