Feature: SpatialData I/O support

[enric-bazz]

This PR ports the changes from the v2-incremental branch into main, primarily to introduce SpatialData I/O support.

Key features

• SpatialData support

  • Accepts SpatialData objects as input, including data read from Zarr stores

  • Produces output as a Zarr-backed SpatialData object

  • Output is controlled via the save_spatialdata flag (default: true), consistent with existing AnnData behavior

  • Supports configurable boundary construction methods:

    • convex_hull
    • delaunay

• 3D segmentation

  • Enabled when a valid z coordinate is present and the feature is activated (default: false)

• Quality value (QV) filtering

  • Default threshold: QV > 20

Provenance of changes

Most of the implementation is derived and adapted from prior changes to the v2-incremental branch, namely:

• commit: 5c4cc5a

• prior PRs:

  • Fix regex filter and table parsing on spatialdata I/O #29
  • Debugged spatialdata writer with refactored shapes #28