spatialdata
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An open and interoperable data framework for spatial omics data
Hi all, I'm starting to use `SpatialData `framework but I'm still missing something. I'm working on this [public CosMx dataset](https://kero.hgc.jp/Breast_Cancer_Spatial.html). I'm able to read it as a `SpatialData` object and...
The `ImageTilesDataset` class cannot be used if the table you want to work with is not called "table", since there are lines where this name is hard-coded, even though the...
Hi, I have been trying to follow the Deep learning example on image tiles tutorial on the spatialdata scverse website. However, I keep running into this error : KeyError: 'coords'....
Hi, making an issue as @giovp suggested. I ran into an issue trying to visualize a specific area of my tissue.  Cropping Spatialdata to a specific area by polygon...
In a test for sequence transformations I had to add some `Identity()` transformations due to a limitation of `_get_current_output_axes()`. See here: https://github.com/scverse/spatialdata/blob/a9fb47776701498a5ecca5e3c5e56a02d59d1224/tests/transformations/test_transformations.py#L435 - [ ] verify that this is not...
During the Ghent Hackathon ([BioHackrXiv here](https://osf.io/preprints/biohackrxiv/uf7d3)) a faster implementation for `vectorize()` has been developed by @hey2homie: https://github.com/saeyslab/VIB_Hackathon_June_2024/blob/main/polygons/polygons_test.ipynb. The implementation also fixes https://github.com/scverse/spatialdata/issues/583, but relies on `opencv`, which is a heavy...
Using [this](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/napari_rois.html#) tutorial for MERFISH data, I found that the output of polygon_query(sdata, my_napari_annotation) does not contain any filtered table, despite my_napari_annotation covering multiple cells. Is there something missing in...
(In reference to https://github.com/scverse/spatialdata/pull/620) This PR imlements an more advanced filtering options than `subset`, allowing to create a new SpatialData object that contains only specific tables, layers, obs keys, var...
closes #556 This PR allows for filtering elements (points, shapes, tables) on instance IDs. For labels I decided just as with the joins to not support it as it is...
