LucaMarconato

Aggregate points by shapes lazily

2

Issue to keep track of this particular aggregation case. Currently when aggregating points by shapes, all the points are loaded into memory. Ideally this would be done incrementally by keeping...

See context here: [#data-structures > JSON in `uns`](https://scverse.zulipchat.com/#narrow/channel/315789-data-structures/topic/JSON.20in.20.60uns.60/with/517500234). Status: - `.attrs` in `pandas` (hence in `geopandas` and `dask.dataframe`) are JSON-serializable, as [shown here](https://github.com/pandas-dev/pandas/issues/51012#issuecomment-1743856513). - In `SpatialData` we can enforce that....

Work in progress, developed together with https://github.com/EricMoerthVis/tissue-map-tools/pull/10

Requires https://github.com/scverse/spatialdata/pull/1006 Todo: - [ ] bump min spatialdata version to 0.7.0 Should fix the install problem https://github.com/scverse/spatialdata/issues/1016 reported by @tischi

speed_up_illustration.ipynb notebook plots all the intermediate plots

1

@Sonja-Stockhaus @timtreis I have tried running the `speed_up_illustration.ipynb` notebook and I have noticed that the all the plots that are made to compute the benchmark are shown. I believe in...

PyArrow OSError: Unexpected end of stream

2

Since the release of `pyarrow 22.0.0` the CI started failing, with errors similar to the one below. Please note that the error doesn't seem to be `spatialdata`-related. [Full CI run...

See suggestions from @ckmah in Zulip: [#spatialdata-dev > unifying readers @ 💬](https://scverse.zulipchat.com/#narrow/channel/443514-spatialdata-dev/topic/unifying.20readers/near/548248316).

`render_points` for categorical columns assumes there is always a table

3

```python from spatialdata.datasets import blobs import spatialdata_plot sdata = blobs() del sdata['table'] sdata.pl.render_points('blobs_points', color='genes').pl.show() ``` The table is not annotating the point, yet if there is no table we get...

Chatted with @timtreis, this could be done with `transfunc` https://github.com/scverse/spatialdata-plot/blob/07e0f0fef4dd3acc09cddb8035b24eec281203a3/src/spatialdata_plot/pl/basic.py#L325 only available for shapes.

`spatialdata` support in `segger`

2

# `spatialdata` support in `segger` Describing use cases and a possible strategy to enable `spatialdata` support. ## Use cases These use cases can be considered as incremental goals, to accomplish...