spatialdata-notebooks issues

Extra examples aggregations

1

"Very work-in-progress" PR where I show some extra examples with aggregation, in particular aggregating into a grid. We could also put that code into a new notebook on rasterization vs...

LucaMarconato

Replace `os.path` with `Path` and "unzip" with `shutil.unpack_archive`

1

@melonora pointed out that this would better generalizes to all platform.

LucaMarconato

Refactor Xenium + Visium paths and use better names

1

- [ ] all the paths used in notebooks `00_xenium_and_visium.ipynb`, `01_xenium_and_visium.ipynb` and `02_xenium_and_visium.ipynb` should be placed in a `config.py` file - [ ] `sandbox.zarr` was a poorly chosen name, rename...

LucaMarconato

Notebook on 3D data and on images from multiple imaging cycles

2

Two related concepts that would be nice to show, and show in the same notebook (from a discussion with @lopollar and @melonora). Sometimes the user has a large 3D image...

LucaMarconato

Add SpaceM datasets

2

This PR adds two SpaceM datasets to the list of example datasets. Additionally, I suggest a notebook that visualizes and explores the contents of the dataset. Descriptions in the notebook...

aeisenbarth

add speed up demonstration of datashader

8

Little benchmark to demonstrate in which cases it is helpful to use datashader to increase rendering speed

Sonja-Stockhaus

documentation

🎨 spatialdata-plot

Update Xenium dataset

The Xenium notebook is using a previous dataset (for XOA 2.0). We should consider using on the following recent datasets, recommended by the 10x team: - [FFPE Human Pancreas with...

LucaMarconato

Check reproducibility of Steinbock and NanoString notebooks on Windows

As reported here for Steinbock (https://github.com/scverse/spatialdata-io/issues/129) and here for NanoString (https://github.com/scverse/spatialdata/issues/637), it looks like that `/` in paths (I guess inside one of the `AnnData` objects), create reproducibility issues on...

LucaMarconato