spatialdata
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scverse
An open and interoperable data framework for spatial omics data
As discussed here https://github.com/scverse/spatialdata/pull/410#discussion_r1430298422 and here https://github.com/scverse/spatialdata/pull/410#discussion_r1441517847, we are considering removing the `region` metadata. We will still write it to disk to be used for cloud applications, but for in-memory...
The function `def read_table_and_validate()` in `src/spatialdata/_io/_utils.py` can be simplified now that the new release of `anndata` handles remote consolidate metadata. See comment in the code. Just a small fix required.
Hi, If you select multiple different regions on a Merscope you get multiple different folders as output. I am trying to combine them into a single object like this: ```...
Zarr has the nice capability of supporting parallel read and write. That means we can have workflows with parallel processing that write data to different parts of the same Zarr...
As mentioned in https://github.com/scverse/napari-spatialdata/issues/67, it would be nice to distribute via conda-forge. I can have a look to see how easy that will be (haven't checked availability of deps on...
Implementation of an apply function for image layers in spatialdata object. Basic usage is similar to squidpy’s apply function, E.g.: ``` def _multiply(image, parameter=2): return image * parameter fn_kwargs =...
Consider adding metadata to the `SpatialData` level. This has been asked by @quentinblampey and will also be required for storing coordinate transformations for this refactoring: https://github.com/scverse/spatialdata/milestone/2
This log: ``` no parent found for : None ``` which appears when reading labels from Zarr should have been disabled by the code in `io_zarr.py`, but somehow these logs...
When writing a SpatialData object which has a column containing string values or empty values, an error is raised. Empty values are a very common use-case: - When two regions...