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WIP: Introduce scene class#583

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WIP: Introduce scene class#583
jo-mueller wants to merge 145 commits into
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jo-mueller:introduce-scene-class

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@jo-mueller jo-mueller commented May 18, 2026 •
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Based on #515

This is a first stab at an ome-zarr-py implementation of the scene metadata/layout that will be part of 0.6. It follows closely and builds upon the design principles of the NgffMultiscales class that's introduced in #515 and mirrors the design of the NgffHCSPlate I propose in #570

TODOs:

  • Add tests
  • Add documentation on how to update/append scenes
  • Keep track internally of underlying graph structures, i.e. in an nx.DiGraph instance?

jo-mueller added 30 commits April 30, 2026 15:41
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feat: add image class
05977bd
@jo-mueller
feat: added reader
c64d653 
feat: added reader
@jo-mueller
feat: pass labels to multiscales writer function
22b11d8 
feat: pass labels to multiscales writer function
@jo-mueller
fix: do not use v06 yet
c92a30d 
fix: do not use v06 yet
@jo-mueller
test: add testcases for class-based writer
ee80edc 
test: add testcases for class-based writer
@jo-mueller
refactor: write scales to zarr group scale<idx>
46cf756 
fix: pass name to multiscales class

feat: add reading/writing

fix: do not use v06 yet

test: add testcases for class-based writer

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refactor: write scales to zarr group scale<idx>

add image class

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remove unused ABC

fix multiscale creation

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use dask utils for rescaling

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more general input coercion

ensure `scaleX` naming for levels

rely on refactoring changes for pyramid creation & write

raise validation error of ndims != data shape

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docstring

pass storage options on to writer function

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move down group check

improve metadata handling

change multiscale path formatting

split into two different classes

compute shapes off actual shapes rather than ideal factors

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use ome-zarr-models-py v06

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add version to export args

correct naming in docstring

code style

remove dead code

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add docstrings

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use CoordinateSystem and Axis from ozmp and pop empty fields

pass name to multiscales class

correct arg passage

Create scene.py

add support for passing additional transformations through class interface

add reading/writing

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remove class conversion methods

add fallback for scales

remove v06 objects

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Delete scene.py

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fix: typesafety

fix: no self-conversion

test: add testcases for class-based writer

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refactor: write scales to zarr group scale<idx>

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refactor: write scales to zarr group scale<idx>

pass name to multiscales class

correct arg passage

Create scene.py

add support for passing additional transformations through class interface

add reading/writing

[pre-commit.ci] auto fixes from pre-commit.com hooks

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remove class conversion methods

add fallback for scales

remove v06 objects

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Delete scene.py

fix: make precommit happy

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fix: typesafety

fix: no self-conversion

test: add testcases for class-based writer

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refactor: write scales to zarr group scale<idx>

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fix: remove 0.6 conversion from reader
5d97ea9 
fix: remove 0.6 conversion from reader
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fix: accept storage options and scale_factors as list[dicts]
fa638cc 
tests: fix tests

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fix: accept storage options and scale_factors as list[dicts]
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tests: calculate expected shape correctly from array shapes
2085929 
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tests: fix typo

tests: calculate expected shape correctly from array shapes

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deps: add ome-zarr-models-py (latest) to dependencies
0444af9 
deps: add ome-zarr-models-py (latest) to dependencies
@jo-mueller
fix: use correct scale folder convention
83027e0 
fix: write label group metadata correctly

fix: use correct scale folder convention
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tests: add writing labels to tests
ebc8171 
tests: remove reference to v06 coordinate systems

tests: removed call to v06 coordinate systems

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fix: make version detector robust for 0.4 metadata

tests: add writing labels to tests
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feat: add labels as class attribute
6effadc 
feat: add labels as class attribute
@jo-mueller
tests: add tests for ingestion of image and data reading
3429b78 
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chore: cast to safe type

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feat: return delayed objects

tests: add tests for ingestion of image and data reading

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refactor: use image classes under the hood
4f5749a 
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refactor: use image classes under the hood

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refactor: rename dims property to axes for consistency
49ccb71
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doc: Add image class to docs
0a393ef 
chore: typo

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chore: fix header levels

chore: fix mutable default values in writers

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chore: make default immutable

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chore: make sure loaded image has a name that's not None
9e96c89 
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chore: make sure loaded image has a name that's not None

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feat: add scale argument to entrypoints
242def2 
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fix: make type-safe

feat: add `scale` argument to entrypoints

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tests: add test for writing scale w/o coordinate transformations
8fd027c 
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chore: remove unused variable

tests: add test for writing scale w/o coordinate transformations

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chore: remove unused variable
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feat: add axes_units kwarg to entrypoints
f173e88 
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chore: update codespell github action

enh: use built-in writer method, not private

enh: pass some missing metadata

enh: do not delay writing metadata

enh: pass scale and units to writer

tests: fix passed and tested scales

enh: type cast

chore: remove unused variable

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chore: remove unused variable

chore: remove redundant error flag

feat: add `axes_units` kwarg to entrypoints

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enh: add backwards compatibility for reading 0.1/0.2/0.3
127dfc4 
enh: add correct translation transforms for legacy reader

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enh: support omero metadata
8330ccb 
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enh: support image-label metadata
78f70bf 
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docs: Update docstrings

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fix: fix docstring

chore: Catch more specific errors

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fix: safer type casting

fix: fix type-declarations

enh: support image-label metadata
@jo-mueller
refactor: Move image classes into submodule
8db9822 
refactor: fix import

refactor: Move image classes into submodule
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tests: add reader tests for new classes
ee90670 
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chore: remove unnnecessary __main__ in test

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tests: fix import

tests: add reader tests for new classes

tests: fix typo
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tests: remove reference to v06 coordinate systems
92ae111 
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feat: return delayed objects
4d72e3a 
chore: typo

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chore: fix header levels

chore: fix mutable default values in writers

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@jo-mueller
fix: default to not using deprecated Scaler
4f49ad8
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enh: do not delay writing metadata
b3892c3
pre-commit-ci Bot and others added 29 commits May 26, 2026 08:41
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@jo-mueller
refactor: move channels-specific kwargs into derived class
b533ce2
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feat: strengthen validation and verbosity of scale/axes/etc wrangling
594118b
@jo-mueller
docs: improve docstrings
70f5b31
@jo-mueller
docs: update classes autodoc
e2217a5
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docs: expand parameters documented in basic write notebook
5f965a7
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chore: precommit fix
d746027
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Merge branch 'introduce-image-class' into introduce-image-class-v06
d68b21a
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Merge branch 'introduce-image-class-v06' into introduce-scene-class
4f7777d
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use latest models and classes
2c5b8fa
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Merge branch 'introduce-scene-class' of https://github.com/jo-mueller…
c5f44b5 
…/ome-zarr-py into introduce-scene-class
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refactor: change naming and use graph building
d611762
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Merge branch 'introduce-scene-class' of https://github.com/jo-mueller…
c1a7675 
…/ome-zarr-py into introduce-scene-class
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update
8d2b586
@jo-mueller
Merge branch 'introduce-scene-class' of https://github.com/jo-mueller…
eb321e3 
…/ome-zarr-py into introduce-scene-class
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@jo-mueller
feat: store images along with paths
4eeb8c8
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Merge branch 'introduce-scene-class' of https://github.com/jo-mueller…
f697e3a 
…/ome-zarr-py into introduce-scene-class
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add mapaxis
e358103
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remove # from colors
9ae38cb
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add transformnd to deps
f823481
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feat: add utility function to discover coordinate system instances
f568199
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@jo-mueller jo-mueller mentioned this pull request Jun 19, 2026
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