napari-spatialdata
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scverse
Interactive visualization of spatial omics data
This PR serves to provide a barebone annotation widget. At the moment only shape annotations are supported but I am to extend this to points and perhaps labels as well....
Hello, great package - keen on integrating spatialdata and this napari interface potentially with some tools I'm developing. **Current Limitation** I notice there is a potentially missed opportunity for improving...
See https://github.com/scverse/napari-spatialdata/issues/150 To give users more control over whether a 3/4-channel image is interpreted and visualized as RGB, channel names now need to be explicitly set to ["r", "g", "b"]....
Hi, Thanks for the fantastic work. I'm running into a problem with saving annotated shapes to my SpatialData object that I was hoping you would be able to help with....
Hi, I am using the viewer to visualize the categorical labels in the table (e.g., cell types) from steinbock-generated data. The viewer plots perfectly, even with a subsetted table. However,...
We should make a function that opens napari-spatialdata with every layer shown (and ideally showing the first gene from var and first column from obs). This function would be used...
updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.3...v0.4.4)
![pre-commit-ci[bot] avatar](https://avatars.githubusercontent.com/in/68672?v=4 "pre-commit-ci[bot] avatar"){kind=avatar}
~When the table misses some instances or contains NaN values, colors are not mapped. Specifically if:~ - ~The table contains less `instances` than the segmentation image in `labels`~ - ~Or...
Hi, after following the tutorial part of [https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/napari_rois.html#extracting-cells-under-the-regions](url), I tried to apply the 'Extracting cells under the regions'. I used this script: `categories = ["unassigned"] + list(filtered_tables.keys())` `n = len(sdata["table"])`...
As discussed with @melonora, currently we don't save napari annotations to disk when Shift+E is pressed, we should re-enabled it (this was automatically done before the incremental IO refactoring, but...