Tim Treis

Function to subset the entire spatialdata object

6

A little bit I started on this PR https://github.com/scverse/squidpy/pull/967 which introduces a function that allows users to subset their entire `SpatialData` objects by certain criteria. The larger goal is to...

Add filter function that subsets the entire object

1

Users can easily break `SpatialData` objects by filtering the contained `AnnData` tables using scanpy - this might remove observations that are still present in other elements, such as `Shapes`. This...

[EXPERIMENTAL]: Integrate cp-measure

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Associated notebook: https://github.com/scverse/squidpy_notebooks/blob/add_cpmeasure_notebook/tutorials/tutorial_cpmeasure.ipynb

Add parameter to `sliding_window` to end up with windows of (approximately) same number of cells

2

Could add a heuristic that tries to optimise the number of cells per window (and unassigned cells) so that on average, most windows have a number of cells assigned that...

From user Jack on Zulip: > Does anyone know how to use spatialdata_io.stereoseq to read BGI's STOmics spatial transcriptomics data? Why is cell.cluster.h5ad required? The count output from SAW doesn't...