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6ce9151
mvp
timtreis Mar 28, 2025
3a82ac8
performance improvement
timtreis Mar 28, 2025
f734634
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 28, 2025
a7d3e6b
Merge branch 'main' into feature/add_cpmeasure
timtreis Mar 28, 2025
9fb24b4
added skimage features
timtreis Mar 28, 2025
4651927
Merge branch 'feature/add_cpmeasure' of github.com:scverse/squidpy in…
timtreis Mar 28, 2025
78ed95c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 28, 2025
c865d57
cleaned up a bit
timtreis Mar 31, 2025
0bc9507
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 31, 2025
60ed223
fixed off-by-one error
timtreis Apr 1, 2025
4fa18f4
Merge branch 'feature/add_cpmeasure' of github.com:scverse/squidpy in…
timtreis Apr 1, 2025
9aade33
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 1, 2025
9ffcb8d
Merge branch 'main' into feature/add_cpmeasure
timtreis Apr 29, 2025
6d056b4
fixed mypy
timtreis Apr 29, 2025
5e11b8d
numba
timtreis Apr 29, 2025
7963e84
pre-alloc types
timtreis Apr 29, 2025
6998a7d
pyproject + numba
timtreis Apr 29, 2025
f7342c8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 29, 2025
b2eb6aa
mypy
timtreis Apr 29, 2025
46be266
Merge branch 'main' into feature/add_cpmeasure
timtreis Apr 30, 2025
86f7373
Merge branch 'main' into feature/add_cpmeasure
timtreis May 25, 2025
c11d3df
Merge branch 'main' into feature/add_cpmeasure
timtreis Sep 9, 2025
b21779f
Merge branch 'main' into feature/add_cpmeasure
timtreis Jan 27, 2026
ce28cff
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 27, 2026
e1327ba
Reorganize CellProfiler features into experimental.im submodule
timtreis Jan 27, 2026
67afe10
Resolve merge conflict - keep im submodule structure
timtreis Jan 27, 2026
c5ab023
Remove unused imports
timtreis Jan 27, 2026
ab62645
Add minimal tests for calculate_image_features
timtreis Jan 27, 2026
61ef03d
Fix tests: add scale parameter for multi-scale data
timtreis Jan 27, 2026
5ba939d
Add tests for bugs described in issue
timtreis Jan 27, 2026
3a2a642
reduced size of sdata obj for testing
timtreis Jan 27, 2026
4c405f7
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 27, 2026
936938f
updated test
timtreis Jan 27, 2026
1375859
merge
timtreis Jan 27, 2026
19d0efb
lint
timtreis Jan 27, 2026
80acb8c
fixed test
timtreis Jan 27, 2026
a41ef20
small refactor + test speedup
timtreis Jan 28, 2026
6b78f0b
added features from legacy function + tests
timtreis Jan 28, 2026
8da641b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 28, 2026
e6da341
Merge branch 'main' into feature/add_cpmeasure
timtreis Apr 7, 2026
baf7f39
Add cell-aware tiling for large image featurization
timtreis Apr 7, 2026
0af69aa
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 7, 2026
64f50c2
Merge branch 'main' into feature/add_cpmeasure
timtreis May 14, 2026
d1b0b95
Finish lazy-tiling refactor and address PR #982 review feedback
timtreis May 14, 2026
9848a6f
Simplify hot paths and reuse existing utilities
timtreis May 14, 2026
d649597
Hoist cp_measure config build out of per-tile worker; bump pin
timtreis May 26, 2026
5bba272
Address review feedback: cap cp-measure pin, soften private signature
timtreis May 26, 2026
205b085
Merge branch 'main' into feature/add_cpmeasure
timtreis May 27, 2026
3a26b3d
Rename compute_cell_info_tiled `chunk` -> `chunk_size`
timtreis May 27, 2026
a8dadcf
Restrict channels= to names; reject integer indices
timtreis May 27, 2026
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2 changes: 2 additions & 0 deletions pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,8 @@ dynamic = [
dependencies = [
"aiohttp>=3.8.1",
"anndata>=0.9",
"centrosome>=1.2.3",
"cp-measure>=0.1.19,<0.2",
"cycler>=0.11",
"dask[array]>=2021.2",
"dask-image>=0.5",
Expand Down
2 changes: 2 additions & 0 deletions src/squidpy/experimental/im/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
WekaParams,
detect_tissue,
)
from ._feature import calculate_image_features
from ._make_tiles import make_tiles, make_tiles_from_spots
from ._qc_image import qc_image
from ._qc_metrics import QCMetric
Expand All @@ -15,6 +16,7 @@
"FelzenszwalbParams",
"QCMetric",
"WekaParams",
"calculate_image_features",
"detect_tissue",
"make_tiles",
"make_tiles_from_spots",
Expand Down
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