spatialdata
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scverse
An open and interoperable data framework for spatial omics data
The time to import `spatialdata` is significant, and can impact some usage scenarios. (This issue is only for tracking. I don't consider it priority at the current stage of the...
Allowing only adata as table is quite cumbersome for my specific need. Any chance that pd.DataFrames will be allowed soon? Thanks!
There are multiple ways (some still to be implemented) to subset/query a `SpatialData` object. Some of these methods are living outside this repo. We need to port them here and...
# Possible bug with scales Bug originally reported here from @aeisenbarth in the context of another issue: https://github.com/scverse/spatialdata/pull/348#issuecomment-1702672491. > Rasterschema.validate(MultiscaleSpatialImage) expects all scale levels to have a transform, but the...
Currently we have the capabilities to compute the pixel to unit scale factor, but doing this is not straightforward due to edge cases that can arise with general coordinate transformations....
Hello, In the documentation [here](https://spatialdata.scverse.org/en/latest/generated/spatialdata.models.Image2DModel.html), `Image2DModel.parse` has a `chunks` argument. Contrary to what suggests the documentation, this argument is only used when creating a `MultiscaleSpatialImage` I was expecting that it...
In `tests/conftest.py` the second multipolygon of the `multipoly` object is invalid, i.e. ``` multipoly = GeoDataFrame( { "geometry": [ MultiPolygon( [ Polygon(((0, 0), (0, 1), (1, 1), (1, 0))), Polygon(((0,...
## Use case As a user, I want to do an image operation (add/subtract, [intersect labels](https://scikit-image.org/docs/stable/api/skimage.segmentation.html#skimage.segmentation.join_segmentations), etc.) which requires two images with **matching shapes**, but they stem from SpatialData elements...
This is a tracking issue for some of the current issues when having a SpatialImage of circa >10 channels in SpatialData: - [ ] **Vizarr, Avivator, Vitessce fail when loading...
Super easy fix. ### Problem The function `to_multiscale()`, which is called by `Image2DModel` and `Image3DModel` when `scale_factors` is a list, calls this code: ```python # IPFS and visualization friendly default...