Tim Treis

Submodular optimization using apricot

3

### What kind of feature would you like to request? New analysis tool: A simple analysis tool you have been using and are missing in `sc.tools`? ### Please describe your...

Allow for spatial perturbation screen analysis

6

Initial data is coming up in which perturbation screens have been analysed using spatial technologies. This workstream should deal with tools to analyse and compare these data. @Zethson

Include more options for niche definitions

11

Currently, squidpy focusses mostly on local [spatial neighborhoods ](https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/tutorial_vizgen_mouse_liver.html#neighborhood-enrichment) for niche analysis purposes. However, there are other definitions which one could use. Including other options could increase tool usage and...

A future extension of the commonly 2D spatial data would be to include "layered" 2.5D data which can then be analysed in 3D. `spatialdata` already allows for storing it, however,...

`sdata.write()` broken -> Reason why GH actions fail

1

MRE ``` from spatialdata.datasets import blobs blobs().write("./blob.zarr") ``` fails with ``` FileNotFoundError: [Errno 2] No such file or directory: '/Users/tim.treis/Documents/GitHub/spatialdata-notebooks/notebooks/examples/blob.zarr/images/blobs_image/0/0/0/0' ``` Inspecting the created file shows that it only goes...

- [x] Image 1 (fixed by https://github.com/scverse/spatialdata-plot/pull/287)  ~Background is taken as shape, should be white. White dots should probably be C~ https://github.com/scverse/spatialdata-plot/pull/323 and https://github.com/scverse/spatialdata-plot/pull/334 - [ ] Image 2...

Use spaco for picking colors?

4

Without having tried it yet, the figure looks convincingly nice. Basically calculates the degree of mixture of all cell type pairs and then maximises contrast based on the given palette....

tbd @Sonja-Stockhaus @LucaMarconato