spatialdata
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scverse
An open and interoperable data framework for spatial omics data
Is there an easy way to rename SpatialElements? For example, an image? Not just in memory, but also on disk? I couldn't really find anything in the docs, except for...
Getting a couple hundred warning of: `/python3.10/site-packages/zarr/creation.py:614: UserWarning: ignoring keyword argument 'read_only' compressor, fill_value = _kwargs_compat(compressor, fill_value, kwargs)` When trying to load a previously saved .zarr in a new enviroment....
**Is your feature request related to a problem? Please describe.** Right now there is no clear showcase of the performance and speed of the SpatialData library, while this is one...
As discussed in https://github.com/scverse/spatialdata/issues/803, the zarr based image data that is currently stored with spatialdata is not compatible with the current OME-Zarr spec and can thus not readily be opened...
Currently we explain how to work with tables with a [notebook](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/tables.html) that has been reported being too technical. We are considering moving the notebook to a technical section of the...
Hi, As far as I understand [SpatialData is currently producing invalid OME-Zarr images](https://imagesc.zulipchat.com/#narrow/channel/328251-NGFF/topic/Not.20identified.20as.20multi-scale.20metadata). I would like to understand why you choose to do this, even though it has obvious disadvantages...
**Is your feature request related to a problem? Please describe.** There are multiple artificial dataset creation functions. It should be clear which ones are most useful and when. **Describe the...
**Is your feature request related to a problem? Please describe.** Current documentation shows small examples. Working on real large datasets varies in some ways and has specific needs: - limiting...
Aim: adding a page in the docs to help methods developers that want to use SpatialData in their tools. The page could cover the following, showing how SpatialData could be...
Just a random note on this: I agree that having SpatialData - level attributes would be super helpful. Beyond that, I think it would be great to be able to...