User story

A SpatialData object can define coordinate systems and transformations between the coordinate systems for any of its spatial elements. When visualizing the data, the user expects these coordinate transformations to be applied automatically.

Preferred solution

Vitessce should use the transformations for all spatial elements, including shapes elements. (Currently, Vitessce uses the transformations when loading SpatialData images and labels elements)

This can be achieved by applying a model matrix that represents the transformation to the X/Y(/Z) coordinates after loading those coordinates from the SpatialData object (but before returning the coordinates from the data loader class's .load() function).

Relevant code and documentation:

• https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/transformations.html#circles-as-shapes
• Current usage of coordinateTransformations for images:

  vitessce/packages/file-types/zarr/src/ome-loaders/OmeZarrLoader.js

  Line 58 in 40fe260

  coordinateTransformations: coordinateTransformationsFromFile,

• vitessce/packages/utils/image-utils/src/ImageWrapper.ts

  Line 74 in 40fe260

  getModelMatrix(): number[] {

• Current code that loads the circle shape coordinates as obsSpots:

  vitessce/packages/file-types/zarr/src/spatialdata-loaders/SpatialDataObsSpotsLoader.js

  Line 28 in 40fe260

  this.locations = this.dataSource.loadNumericForDims(getCoordsPath(path), dims);

Possible alternatives