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Support SpatialData

Open keller-mark opened this issue 2 years ago • 3 comments

User story

We want to support loading SpatialData objects, including local SpatialData objects.

Preferred solution

To do this, we need an analog of the AnnDataWrapper class but for SpatialData. This wrapper class allows us to:

  • know which parts/keys of the object should be used in the configuration, and how those keys should map to Vitessce concepts
  • Serve the local Zarr directory on localhost so that the widget JS code can request the data via HTTP

Relevant code/documentation:

  • https://github.com/vitessce/vitessce-python/blob/main/vitessce/wrappers.py
  • Documentation for AnnDataWrapper class https://vitessce.github.io/vitessce-python/api_data.html#vitessce.wrappers.AnnDataWrapper
  • Usage of AnnDataWrapper class in example notebook: https://vitessce.github.io/vitessce-python/notebooks/widget_brain.html#4.2.-Add-a-dataset-to-the-VitessceConfig-instance

keller-mark avatar Jan 31 '23 19:01 keller-mark

https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html

keller-mark avatar Aug 15 '23 01:08 keller-mark

Depends on https://github.com/vitessce/vitessce/pull/1728

keller-mark avatar Jan 24 '24 21:01 keller-mark

We will also want to embed an example notebook in the documentation that demonstrates how to use the implementation. These notebooks are located at https://github.com/vitessce/vitessce-python/tree/main/docs/notebooks

keller-mark avatar Apr 01 '24 12:04 keller-mark