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NGFF Multiscales and Scene round-tripping - #1286

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Tomaz-Vieira wants to merge 43 commits into

scverse:mainfrom

Tomaz-Vieira:ngff_io

Draft

NGFF Multiscales and Scene round-tripping#1286
Tomaz-Vieira wants to merge 43 commits into
scverse:mainfrom
Tomaz-Vieira:ngff_io

Commits on Sep 15, 2026
- Transformation manager foundation (#1164)
  ajkswamy
  committed
  75e5a44
Commits on Oct 1, 2026
- Transformation manager foundation (#1164)
  
  ajkswamy
  authored and
  Tomaz-Vieira
  committed
  519a3e2
- Creates the graph module based on the Ngff* classes
  Tomaz-Vieira
  committed
  3a47dd4
- addresses some PR comments, simplifies MapAxis
  Tomaz-Vieira
  committed
  e4ff532
- Adds ProjectAxisEdge, makes inverse return optional
  Tomaz-Vieira
  committed
  796d557
- Moves exceptions to exceptions.py, edge names default to None
  Tomaz-Vieira
  committed
  406375d
- Use custom exceptions everywhere, adds Raises to docstrings
  Tomaz-Vieira
  committed
  db250b4
- Fix Affine.from_affine_matrix slicing]
  Tomaz-Vieira
  committed
  28e13c9
- Fix coords bug when reading from OMEZarrMultiscale. Some cleanup
  Tomaz-Vieira
  committed
  d7da440
- Adds test for parsing OMEZarrMultiscale
  Tomaz-Vieira
  committed
  7384dd8
- Adds transformations tests, fixes some slicing bugs
  
  Tomaz-Vieira
  and
  claude
  committed
  9bf5b28
- Adds basic .sel test to parsed multiscale
  Tomaz-Vieira
  committed
  14d5b71
- Removes unused class
  Tomaz-Vieira
  committed
  7b346a1
- Adds more slicing tests to parsed multiscales
  Tomaz-Vieira
  committed
  e3fbe7e
- Adds/fixes comments in try_parse_ngff06_multiscales
  Tomaz-Vieira
  committed
  ae02611
- Removes to_model methods for now
  Tomaz-Vieira
  committed
  7ca1476
- Moves AxisParsingException to exceptions.py
  Tomaz-Vieira
  committed
  13b2a3d
- Moves AxisParsingException back into vert.py to prevent circular imports
  Tomaz-Vieira
  committed
  ebb6f8a
- Fixes docstrings, list exceptions in "Raises"
  
  Tomaz-Vieira
  and
  claude
  committed
  bf2178f
- Incorporates parse_project_axis
  Tomaz-Vieira
  committed
  fd74830
- Fixes parsing translatiion model getting bad name
  
  Tomaz-Vieira
  and
  claude
  committed
  1177ee4
- Adds test for parsing *Edge transforms from ngff
  
  Tomaz-Vieira
  and
  claude
  committed
  4fe7f8a
- Fixes dependencies on ome-zarr and ome-zarr-models
  Tomaz-Vieira
  committed
  dcc436b
- Cleans up transform_points for rotation and affine
  Tomaz-Vieira
  committed
  cec5085
- Fixes renamed fields in ome-zarr-models
  Tomaz-Vieira
  committed
  8327b55
- Use frozen dataclasses for CoordSystems and Axis. Fix MapAxisEdge
  Tomaz-Vieira
  committed
  25cfc73
- Enforces Rotation matrix is orthonormal with det==1
  Tomaz-Vieira
  committed
  45fb0ff
- Bump xarray so we can use RangeIndex
  Tomaz-Vieira
  committed
  09c8984
- Removes try-from_model_or_defaul for now
  Tomaz-Vieira
  committed
  9de2b15
- Emits warning on AffineEdge.inverse when condition is big
  Tomaz-Vieira
  committed
  155c78a
- Uses matrix in exceptions
  Tomaz-Vieira
  committed
  1298563
Commits on Oct 16, 2026
- Merge branch 'main' into transformation_manager
  ajkswamy
  committed
  c346f44
Commits on Oct 21, 2026
- [WIP] Restores from zarr accident
  Tomaz-Vieira
  committed
  16d1b06
- Return SpatialData and Spaces which can be merged with each other
  Tomaz-Vieira
  committed
  7c1bff6
- Fix loading graph verts in correct order for multiscales and scene
  Tomaz-Vieira
  committed
  30bcf75
- Fixes more dumping issues
  Tomaz-Vieira
  committed
  5755f1e
Commits on Oct 22, 2026
- More dump fixes. Upstream ome-zarr-py needs some work
  Tomaz-Vieira
  committed
  268bd99
- Dumb fix for 'discrete' coming form ngff axes
  Tomaz-Vieira
  committed
  a575456
- adds more asserts to scene tests, no passing yet
  Tomaz-Vieira
  committed
  61a8083
- Reanems FutureSpatialData.__graph to just _graph. Fix tests
  Tomaz-Vieira
  committed
  526de05
- Adds CsVert.__str__
  Tomaz-Vieira
  committed
  61ebeff
Commits on Oct 23, 2026
- Adds a test for parsing OMEZarrScene
  Tomaz-Vieira
  committed
  2d99e5f
Commits on Oct 25, 2026
- Adds use OMEZzarrMultiscale(scale_factors=...) in MultiscaleDumper.dump
  Tomaz-Vieira
  committed
  657693e

Commits

Commits on Sep 15, 2026

Commits on Oct 1, 2026

Commits on Oct 16, 2026

Commits on Oct 21, 2026

Commits on Oct 22, 2026

Commits on Oct 23, 2026

Commits on Oct 25, 2026