LLehner

@giovp I did apply the changes, there were some minor things i had to change though. It's on the spatialde repo.

Hi @amorje thank you for your interest in Squidpy. I couldn't reproduce your error with the latest version 1.3.0 of Squidpy. Which Squidpy version are you running?

This functionality has been added with #591.

Hi @jwrth and @almaan the squidpy plotting module now allows to plot gene expression (or any other variable) to be plotted against the distance to a user-defined anchor point. You...

```squidpy.tl.var_by_distance()``` for calculating the distances to an anchor point and ```squidpy.pl.var_by_distance()``` for visualization. And example will be made available soon with the next squidpy release.

Hi @wangjiawen2013, when using squidpy's ```read.visium()``` it should already be possible to read in both spaceranger 1.0 and 2.0 files and plot the data correctly. Scanpy's ```read_visium()``` is now also...

Closing this now, because `sq.read.visium()` works and there is also the option to read visium files using [spatialdata-io](https://github.com/scverse/spatialdata-io) with `spatialdata_io.visium()`. For the spatialdata-io method description see [here](https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.visium.html).

**Neighborhood based:** - [monkeybread](https://monkeybread.readthedocs.io/en/latest/generated/monkeybread.calc.cellular_niches.html#monkeybread.calc.cellular_niches) (clustering of neighborhood profiles) - [CellCharter](https://www.biorxiv.org/content/10.1101/2023.01.10.523386v2) (performs dimreduction, neighborhood calculation, aggregation and clustering) - [UTAG](https://www.nature.com/articles/s41592-022-01657-2) - [SpaGene](https://genome.cshlp.org/content/32/9/1736.full.pdf+html) **VI and Bayesian methods:** - [DestVI](https://www.nature.com/articles/s41587-022-01272-8) ("Unlike other methods,...

Hi @GhobrialMoheb, for loading CosMx datasets efficiently I would highly recommend to use [spatialdata-io](https://github.com/scverse/spatialdata-io), which has a reader for CosMx called `cosmx()`.

@timtreis this function now returns an `anndata` object, which is i think simplifies further processing, compared to storing the new count matrix somewhere in `.varm` or `.uns`. Because if we...