spatialdata
spatialdata copied to clipboard
scverse
An open and interoperable data framework for spatial omics data
Observed by @quentinblampey. Seems like `zonal_stats()` deals with the `list` case, but not `pd.GroupBy.agg()` (used in the vector by vector case).
As described in issue #404, it is useful to have attributes at the `SpatialData` object level. This will also be useful in Sopa, to simplify the API. Usage: ```python import...
Add default argument `shortest_path: bool=True` in `get_transformation_between_coordinate_systems()`
CC @quentinblampey We should add the argument mentioned above since otherwise the user faces an error (prompting to choose between different transformation paths) also in cases when this is not...
I'm looking for even just the simplest case, i.e. fixing a z-location and visualizing x, y coordinates in 2D. I tried naively with spatialdata-plot, i.e. just `sdata.pl.render_images("image", channel="DAPI").pl.show()`, but that...
Hi, here I tried to register the DAPI staining images between nanostring and xenium, and apply that transformation to the segmentation masks, the images aligns well in the napari, however,...
updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.3 → v0.6.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.6.3...v0.6.7)
![pre-commit-ci[bot] avatar](https://avatars.githubusercontent.com/in/68672?v=4 "pre-commit-ci[bot] avatar"){kind=avatar}
**Is your feature request related to a problem? Please describe.** A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] It'd be elegant to...
Hello, I am contacting you about the “not self-contained” message when saving sdata to a new location. Here is the example: ``` import spatialdata as sd from spatialdata.datasets import blobs...
Follow up PR for https://github.com/scverse/spatialdata/pull/588, see discussion https://github.com/scverse/spatialdata/issues/597 for relabeling in case output data is a labels layer (i.e. `dims` does not contain `c`) via use of a bit shift.
**Is your feature request related to a problem? Please describe.** - `spatialdata.aggregate` does not support 3D, - `spatialdata.aggregate` can be slow on large images. - `spatialdata.aggregate` does not allow aggregation...