[EXPERIMENTAL]: Integrate cp-measure by timtreis · Pull Request #982 · scverse/squidpy

timtreis · 2025-03-28T16:47:13Z

Associated notebook: https://github.com/scverse/squidpy_notebooks/blob/add_cpmeasure_notebook/tutorials/tutorial_cpmeasure.ipynb

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timtreis · 2025-05-16T12:22:20Z

Note to self:

Doesn't correctly parse str names of channels
INFO Calculating 'cpmeasure' correlation features between channels '0' and '1'.
Should show, for permutations, the total number of iterations (in general, the progress bar should contain a (step n out m) readout so one can know how far in the featurisation is. Can easily take more than a day given the amount of cells and cpu_cores. Should also maybe show the total runtime so far for the steps that are done
Fails if labels and image don't have the same dimensions, despite transformation to align them

pakiessling · 2025-10-02T08:18:53Z

Tried it out and it worked very well!

One quality of life feature would be the ability to specify channels that should be measured.

Often times there are channels that are not informative / used only for segmentation and those slow down the calculations.

pakiessling · 2025-10-09T12:04:10Z

Ah I noticed another thing.

For the created morphology table .uns["spatialdata_attrs"] needs to be set, otherwise this runs into problem when querying the Spatialdata afterwards.

- Resolved dependency conflicts (updated to zarr>=3) - Moved exp module to experimental to align with main - Integrated CellProfiler features into experimental module - Added centrosome and cp_measure dependencies

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Moved calculate_image_features from experimental._feature to experimental.im._feature to follow the existing module structure. Now accessible as squidpy.experimental.im.calculate_image_features

- Test basic feature calculation with shapes - Test copy vs inplace behavior - Test error cases for invalid keys - Uses sdata_hne fixture with skimage:label for fast execution

codecov · 2026-01-27T13:13:38Z

Codecov Report

❌ Patch coverage is 58.67159% with 224 lines in your changes missing coverage. Please review.
✅ Project coverage is 72.87%. Comparing base (76ca03f) to head (0af69aa).

Files with missing lines	Patch %	Lines
src/squidpy/experimental/im/_feature.py	51.54%	185 Missing and 35 partials ⚠️
src/squidpy/experimental/im/_tiling.py	95.45%	2 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #982      +/-   ##
==========================================
- Coverage   74.05%   72.87%   -1.19%     
==========================================
  Files          39       41       +2     
  Lines        6495     7037     +542     
  Branches     1122     1249     +127     
==========================================
+ Hits         4810     5128     +318     
- Misses       1230     1417     +187     
- Partials      455      492      +37

Files with missing lines	Coverage Δ
src/squidpy/experimental/im/_tiling.py	`95.45% <95.45%> (ø)`
src/squidpy/experimental/im/_feature.py	`51.54% <51.54%> (ø)`

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LucaMarconato · 2026-01-27T14:02:07Z

Looking forward to this PR 👀🥸

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Introduces _tiling.py with build_tile_specs() and extract_tile() that split a label image into overlapping tiles where each cell is assigned to exactly one tile by centroid. Non-owned cells are zeroed out so downstream processing never double-counts. Includes 31 tests: deterministic brick-pattern grid (touching and non-touching), coverage verification, and visual regression tests. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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timtreis · 2026-04-08T09:04:38Z

Refactoring in anticipation of afermg/cp_measure#38 being merged so we can upstream behaviour.

timtreis and others added 4 commits March 28, 2025 15:39

mvp

6ce9151

performance improvement

3a82ac8

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Merge branch 'main' into feature/add_cpmeasure

a7d3e6b

timtreis marked this pull request as draft March 28, 2025 16:52

timtreis and others added 3 commits March 28, 2025 22:38

added skimage features

9fb24b4

Merge branch 'feature/add_cpmeasure' of github.com:scverse/squidpy in…

4651927

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timtreis added enhancement ✨ New feature or request image 🔬 squidpy2.0 Everything releated to a Squidpy 2.0 release sdata compat 🌌 release-added labels Mar 28, 2025

timtreis mentioned this pull request Mar 28, 2025

MVP for morpohology module #866

Closed

timtreis and others added 5 commits March 31, 2025 18:40

cleaned up a bit

c865d57

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fixed off-by-one error

60ed223

Merge branch 'feature/add_cpmeasure' of github.com:scverse/squidpy in…

4fa18f4

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timtreis mentioned this pull request Apr 1, 2025

calculate_image_features() error with tutorial data #826

Open

timtreis and others added 8 commits April 29, 2025 15:31

Merge branch 'main' into feature/add_cpmeasure

9ffcb8d

fixed mypy

6d056b4

numba

5e11b8d

pre-alloc types

7963e84

pyproject + numba

6998a7d

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mypy

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Merge branch 'main' into feature/add_cpmeasure

46be266

timtreis mentioned this pull request May 9, 2025

Expected width to be in interval error im.calculate_image_features #989

Closed

timtreis marked this pull request as ready for review September 11, 2025 20:15

timtreis mentioned this pull request Oct 1, 2025

Measuring large SpatialData objects afermg/cp_measure#25

Closed

timtreis mentioned this pull request Oct 30, 2025

ValueError: Expected height to be in interval #1046

Closed

timtreis and others added 6 commits January 27, 2026 13:46

Merge branch 'main' into feature/add_cpmeasure

b21779f

- Resolved dependency conflicts (updated to zarr>=3) - Moved exp module to experimental to align with main - Integrated CellProfiler features into experimental module - Added centrosome and cp_measure dependencies

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

ce28cff

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Reorganize CellProfiler features into experimental.im submodule

e1327ba

Moved calculate_image_features from experimental._feature to experimental.im._feature to follow the existing module structure. Now accessible as squidpy.experimental.im.calculate_image_features

Resolve merge conflict - keep im submodule structure

67afe10

Remove unused imports

c5ab023

Add minimal tests for calculate_image_features

ab62645

- Test basic feature calculation with shapes - Test copy vs inplace behavior - Test error cases for invalid keys - Uses sdata_hne fixture with skimage:label for fast execution

timtreis added 2 commits January 27, 2026 14:22

Fix tests: add scale parameter for multi-scale data

61ef03d

Add tests for bugs described in issue

5ba939d

timtreis and others added 12 commits January 27, 2026 15:52

reduced size of sdata obj for testing

3a2a642

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updated test

936938f

merge

1375859

lint

19d0efb

fixed test

80acb8c

small refactor + test speedup

a41ef20

added features from legacy function + tests

6b78f0b

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Merge branch 'main' into feature/add_cpmeasure

e6da341

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This was referenced Apr 10, 2026

Add tiling QC metric for tile-boundary segmentation artifacts #1156

Closed

Add tiling QC metric for tile-boundary segmentation artifacts #1157

Open

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[EXPERIMENTAL]: Integrate cp-measure#982

[EXPERIMENTAL]: Integrate cp-measure#982
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