Mark Keller

Use anywidget-based IPC for zarr gets which do not require serving data on localhost

1

This change enables using the Vitessce widget in HPC situations, on Google Colab, in VSCode, and in HuBMAP Workspaces with data that is local to the Python kernel. Uses the...

Add option for widget to communicate directly with Zarr store (no local HTTP server)

2

TODO: add `_store` parameters for all Zarr-based wrapper classes - [x] `adata_store` parameter for AnnDataWrapper (#322) - [ ] `img_store` parameter for `ImageOmeZarrWrapper` - [ ] `img_store` parameter for `ObsSegmentationsOmeZarrWrapper`...

- Use all chromosomes present in input dataframe. - Emit warning about chromosomes that are contained in assembly but not in the input dataframe to catch cases in which users...

Notebook for creating small test dataset based on MCMICRO exemplar dataset

TODO: use spatialBeta view and add featureList/obsSets views

Convert spatialdata-plot plotting tree to Vitessce config

1

https://github.com/scverse/spatialdata-plot/blob/88f692848e06907fe86a8ac3bc0f689b1a114479/src/spatialdata_plot/pl/basic.py#L139 spatialdata-plot has the goal to support different plotting backends. If we can convert the plotting tree generated by spatialdata-plot to a Vitessce configuration, we can add Vitessce as a...

https://squidpy.readthedocs.io/en/stable/api.html#module-squidpy.datasets

We should aim to have tutorials / examples for how to visualize data from the most-commonly used sequencing instruments and their associated data processing pipelines. One of these instruments /...

Fixes #276 Plan to release in new major version - make upgrade guide docs page?