scikit-image 0.25.2 (2025-02-18)

We're happy to announce the release of scikit-image 0.25.2!

Bug Fixes

Handle random degenerate case in skimage.graph.cut_normalized gracefully (#7675 <https://github.com/scikit-image/scikit-image/pull/7675>_).
In skimage.feature.BRIEF, copy keypoints if necessary to preserve contiguity (#7692 <https://github.com/scikit-image/scikit-image/pull/7692>_).
Revert a previous fix to skimage.segmentation.watershed that unintentionally changed the algorithm's behavior for markers placed at maxima in the image. We decided that the behavior originally reported as a bug (gh-6632), is not actually one (#7702 <https://github.com/scikit-image/scikit-image/pull/7702>_).

Documentation

Improve docstring of skimage.restoration.rolling_ball (#7682 <https://github.com/scikit-image/scikit-image/pull/7682>_).

Infrastructure

Only run the job if the PR got merged (vs merely closed) (#7679 <https://github.com/scikit-image/scikit-image/pull/7679>_).
Fix typo in GH workflow (#7681 <https://github.com/scikit-image/scikit-image/pull/7681>_).
Refactor GitHub's CI config and helper scripts (#7672 <https://github.com/scikit-image/scikit-image/pull/7672>_).
Use pytest config in pyproject.toml in CI (#7555 <https://github.com/scikit-image/scikit-image/pull/7555>_).
Lower CI build verbosity (#7688 <https://github.com/scikit-image/scikit-image/pull/7688>_).
Port testing on Windows from Azure CI to GitHub's CI (#7687 <https://github.com/scikit-image/scikit-image/pull/7687>_).
CI cleanup (#7693 <https://github.com/scikit-image/scikit-image/pull/7693>_).
Simultaneously resolve all dependencies; add pip caching (#7690 <https://github.com/scikit-image/scikit-image/pull/7690>_).
Reenable graph reproducibility test (#7694 <https://github.com/scikit-image/scikit-image/pull/7694>_).
Give milestone labeler necessary permissions (#7695 <https://github.com/scikit-image/scikit-image/pull/7695>_).
Milestone labeler permission not needed (#7696 <https://github.com/scikit-image/scikit-image/pull/7696>_).
Fix 313t wheel build (#7699 <https://github.com/scikit-image/scikit-image/pull/7699>_).

Maintenance

Include a missing image in meson.build so they are included in the wheel (#7660 <https://github.com/scikit-image/scikit-image/pull/7660>_).
Add zizmor to pre-commit; address GH workflow issues raised (#7662 <https://github.com/scikit-image/scikit-image/pull/7662>_).

Contributors

6 authors added to this release (alphabetically):

Jarrod Millman (@jarrodmillman <https://github.com/jarrodmillman>_)
Lars Grüter (@lagru <https://github.com/lagru>_)
Marianne Corvellec (@mkcor <https://github.com/mkcor>_)
Matthew Brett (@matthew-brett <https://github.com/matthew-brett>_)
Orion Poplawski (@opoplawski <https://github.com/opoplawski>_)
Stefan van der Walt (@stefanv <https://github.com/stefanv>_)

8 reviewers added to this release (alphabetically):

Jarrod Millman (@jarrodmillman <https://github.com/jarrodmillman>_)
Juan Nunez-Iglesias (@jni <https://github.com/jni>_)
Lars Grüter (@lagru <https://github.com/lagru>_)
Marianne Corvellec (@mkcor <https://github.com/mkcor>_)
Mark Harfouche (@hmaarrfk <https://github.com/hmaarrfk>_)
Matthew Brett (@matthew-brett <https://github.com/matthew-brett>_)
Ralf Gommers (@rgommers <https://github.com/rgommers>_)
Stefan van der Walt (@stefanv <https://github.com/stefanv>_)

These lists are automatically generated, and may not be complete or may contain duplicates.

scikit-image 0.25.1 (2025-01-26)

We're happy to announce the release of scikit-image 0.25.1!

Bug Fixes

Include centroid in __all__ of the PYI file in skimage.measure (#7652 <https://github.com/scikit-image/scikit-image/pull/7652>_).
Improve numerical stability of blur_effect (#7643 <https://github.com/scikit-image/scikit-image/pull/7643>_).
Because under-determined fits are unreliable, skimage.measure.EllipseModel will now warn and return False (no fit) when fewer than 5 data points are provided (#7648 <https://github.com/scikit-image/scikit-image/pull/7648>_).
Explicitly upcast data with dtype float16 to float32 in skimage.segmentation.random_walker; this fixes passing float16 on NumPy 1.26 (#7655 <https://github.com/scikit-image/scikit-image/pull/7655>_).

Documentation

Don't use removed QuadContourSet.collections in gallery example (#7638 <https://github.com/scikit-image/scikit-image/pull/7638>_).
Change old import convention in the gallery examples (#7630 <https://github.com/scikit-image/scikit-image/pull/7630>_).

Infrastructure

Make apigen.py work with editable hooks (#7647 <https://github.com/scikit-image/scikit-image/pull/7647>_).
Build Linux ARM wheels natively (#7664 <https://github.com/scikit-image/scikit-image/pull/7664>_).

Maintenance

Infer floating point type for sigma parameter (#7637 <https://github.com/scikit-image/scikit-image/pull/7637>_).
In skimage.segmentation.active_contour, change the type of the default argument for w_line to indicate it is a float (#7645 <https://github.com/scikit-image/scikit-image/pull/7645>_).
Temporarily disable parallel building of gallery (#7656 <https://github.com/scikit-image/scikit-image/pull/7656>_).
[pre-commit.ci] pre-commit autoupdate (#7649 <https://github.com/scikit-image/scikit-image/pull/7649>_).
Skip flaky test on azure (#7669 <https://github.com/scikit-image/scikit-image/pull/7669>_).

Contributors

8 authors added to this release (alphabetically):

@michaelbratsch <https://github.com/michaelbratsch>_
@scrimpys <https://github.com/scrimpys>_
Jarrod Millman (@jarrodmillman <https://github.com/jarrodmillman>_)
Jigyasu (@jgyasu <https://github.com/jgyasu>_)
kwikwag (@kwikwag <https://github.com/kwikwag>_)
Lars Grüter (@lagru <https://github.com/lagru>_)
Marianne Corvellec (@mkcor <https://github.com/mkcor>_)
Stefan van der Walt (@stefanv <https://github.com/stefanv>_)

8 reviewers added to this release (alphabetically):

@michaelbratsch <https://github.com/michaelbratsch>_
Dan Schult (@dschult <https://github.com/dschult>_)
Jarrod Millman (@jarrodmillman <https://github.com/jarrodmillman>_)
Jigyasu (@jgyasu <https://github.com/jgyasu>_)
Lars Grüter (@lagru <https://github.com/lagru>_)
Marianne Corvellec (@mkcor <https://github.com/mkcor>_)
Ruth Comer (@rcomer <https://github.com/rcomer>_)
Stefan van der Walt (@stefanv <https://github.com/stefanv>_)

These lists are automatically generated, and may not be complete or may contain duplicates.

scikit-image 0.25.0 (2024-12-13)

We're happy to announce the release of scikit-image 0.25.0!

New Features

Add the new Gray-Level Co-occurrence Matrix (GLCM) properties "mean", "variance", "standard deviation" and "entropy" to skimage.feature.texture.graycoprops (#7375 <https://github.com/scikit-image/scikit-image/pull/7375>_).
Add the new skimage.morphology.footprint_rectangle supporting generation of rectangular or hyper-rectangular footprints in one function (#7566 <https://github.com/scikit-image/scikit-image/pull/7566>_).

API Changes

Complete the deprecation of and remove skimage.feature.plot_matches. Use skimage.feature.plot_matched_features going forward (#7487 <https://github.com/scikit-image/scikit-image/pull/7487>_).
Deprecate skimage.io.imshow, skimage.io.imshow_collection and skimage.io.show. Please use matplotlib, napari, etc. to visualize images (#7508 <https://github.com/scikit-image/scikit-image/pull/7508>_).
Remove deprecated skimage.morphology.skeletonize_3d; use skimage.morphology.skeletonize instead (#7572 <https://github.com/scikit-image/scikit-image/pull/7572>_).
Deprecate skimage.io plugin infrastructure (#7353 <https://github.com/scikit-image/scikit-image/pull/7353>_).
Switched to using the scipy.sparse array interface. For more details, see the note about the new scipy.sparse array interface here (#7576 <https://github.com/scikit-image/scikit-image/pull/7576>_).
Deprecate skimage.morphology.rectangle in favor of the new function skimage.morphology.footprint_rectangle (#7566 <https://github.com/scikit-image/scikit-image/pull/7566>_).
Deprecate skimage.morphology.cube in favor of the new function skimage.morphology.footprint_rectangle (#7566 <https://github.com/scikit-image/scikit-image/pull/7566>_).
Deprecate skimage.morphology.square in favor of the new function skimage.morphology.footprint_rectangle (#7566 <https://github.com/scikit-image/scikit-image/pull/7566>_).

Enhancements

Improve numerical stability of skimage.morphology.local_minima for extremely small floats (#7534 <https://github.com/scikit-image/scikit-image/pull/7534>_).
Allow passing a sequence of colors to the parameter matches_color in skimage.feature.plot_matched_features (#7541 <https://github.com/scikit-image/scikit-image/pull/7541>_).
Make sure that skimage.feature.plot_matched_features uses the same random colors, if matches_color isn't provided explicitly (#7541 <https://github.com/scikit-image/scikit-image/pull/7541>_).

Performance

skimage.feature.peak_local_max will now skip unnecessary distance computations in the case of min_distance=1. This results in performance improvements to functions like skimage.feature.blob_dog, skimage.feature.blob_log, skimage.feature.blob_doh and skimage.feature.corner_peaks that call peak_local_max internally (#7548 <https://github.com/scikit-image/scikit-image/pull/7548>_).
In skimage.featurepeak_local_max, skip unnecessary check for cases where min_distance > 1 is passed (#7548 <https://github.com/scikit-image/scikit-image/pull/7548>_).

Bug Fixes

Ensure that skimage.morphology.remove_objects_by_distance doesn't fail if the given integer dtype cannot be safely cast to the architecture specific size of intp, e.g. on i386 architectures (#7453 <https://github.com/scikit-image/scikit-image/pull/7453>_).
Fix degeneracy in skimage.draw.ellipsoid_stats when all semi-axes have the same length (#7473 <https://github.com/scikit-image/scikit-image/pull/7473>_).
Prevent skimage.morphology.thin from accidentally modifying the input image in case it is of dtype uint8 (#7469 <https://github.com/scikit-image/scikit-image/pull/7469>_).
Fix numerical precision error in skimage.measure.ransac. In some cases, ransac was stopping at the first iteration (#7065 <https://github.com/scikit-image/scikit-image/pull/7065>_).
Fix numerical precision error in skimage.measure.ransac; very small probabilities lead to -0 number of max trials (#7496 <https://github.com/scikit-image/scikit-image/pull/7496>_).
Ensure that RegionProperties objects returned by skimage.measure.regionprops can be deserialized with pickle (#7569 <https://github.com/scikit-image/scikit-image/pull/7569>_).
Fix edge case where setting watershed_lines=True in skimage.segmentation.watershed resulted in an incorrect solution (#7071 <https://github.com/scikit-image/scikit-image/pull/7071>_).
Fix the behavior of skimage.segmentation.watershed when the markers don't align with local minima by making sure every marker is evaluated before successive pixels (#7071 <https://github.com/scikit-image/scikit-image/pull/7071>_).
Fix dtype promotion in skimage.segmentation.join_segmentations if numpy.uint is used with NumPy<2 (#7292 <https://github.com/scikit-image/scikit-image/pull/7292>_).

Documentation

In skimage.morphology.skeletonize, clarify the expected image dtypes and how objects of different intensities are handled (#7456 <https://github.com/scikit-image/scikit-image/pull/7456>_).
Fix example section in docstring of skimage.feature.graycomatrix (#7297 <https://github.com/scikit-image/scikit-image/pull/7297>_).
Use conda-forge consistently in instructions for setting up the development environment (#7483 <https://github.com/scikit-image/scikit-image/pull/7483>_).
Use new CITATION.cff instead of CITATION.bib (#7505 <https://github.com/scikit-image/scikit-image/pull/7505>_).
Use correct spin test --coverage in contribution guide (#7515 <https://github.com/scikit-image/scikit-image/pull/7515>_).
Tweak advice to new developers; remove AI warning (#7522 <https://github.com/scikit-image/scikit-image/pull/7522>_).
Rework installation instructions (#7434 <https://github.com/scikit-image/scikit-image/pull/7434>_).
Improve the description of the image parameter in skimage.restoration.richardson_lucy (#7477 <https://github.com/scikit-image/scikit-image/pull/7477>_).
Account for empty arrays when counting segments per contour level in gallery example "Segment human cells (in mitosis)" (#7551 <https://github.com/scikit-image/scikit-image/pull/7551>_).
Fix typo in morphology doc (#7606 <https://github.com/scikit-image/scikit-image/pull/7606>_).
Change type description of parameter radius in skimage.morphology.ball from int to float (#7627 <https://github.com/scikit-image/scikit-image/pull/7627>_).

Infrastructure

Fix CI tests with minimal dependencies and make dependency resolution more robust (#7462 <https://github.com/scikit-image/scikit-image/pull/7462>_).
Add CI to test scikit-image against free-threaded Python 3.13 (#7463 <https://github.com/scikit-image/scikit-image/pull/7463>_).
Address autosummary.import_cycle warning (#7486 <https://github.com/scikit-image/scikit-image/pull/7486>_).
Temporarily exclude Dask 2024.8.0 to fix CI (#7493 <https://github.com/scikit-image/scikit-image/pull/7493>_).
Uncomment currentmodule directive again (#7492 <https://github.com/scikit-image/scikit-image/pull/7492>_).
Add CI to release nightly free-threaded wheels (#7481 <https://github.com/scikit-image/scikit-image/pull/7481>_).
Update deprecated configuration (#7501 <https://github.com/scikit-image/scikit-image/pull/7501>_).
Bump spin version to 0.11 (#7507 <https://github.com/scikit-image/scikit-image/pull/7507>_).
Ensure only a single type: label is present in PRs (#7512 <https://github.com/scikit-image/scikit-image/pull/7512>_).
Update pydata-sphinx-theme (#7511 <https://github.com/scikit-image/scikit-image/pull/7511>_).
Fix OpenBLAS s_cmp unresolved symbol error, update Emscripten CI testing (#7525 <https://github.com/scikit-image/scikit-image/pull/7525>_).
Render paragraphs in dormant message (#7549 <https://github.com/scikit-image/scikit-image/pull/7549>_).
Build sphinx documentation with parallel jobs (#7579 <https://github.com/scikit-image/scikit-image/pull/7579>_).
Don't check test coverage in CI (#7594 <https://github.com/scikit-image/scikit-image/pull/7594>_).
Explicitly setup conda on macos for wheel building (#7608 <https://github.com/scikit-image/scikit-image/pull/7608>_).

Maintenance

Verify all artifacts that have been attested by looping over them in CI (#7447 <https://github.com/scikit-image/scikit-image/pull/7447>_).
Update circleci-artifacts-redirector-action that moved to the Scientific Python org (#7446 <https://github.com/scikit-image/scikit-image/pull/7446>_).
Use NumPy 2.0 stable to build packages (#7451 <https://github.com/scikit-image/scikit-image/pull/7451>_).
FIX Use python3 in Meson version script shebang (#7482 <https://github.com/scikit-image/scikit-image/pull/7482>_).
Refactored tests for skeletonize (#7459 <https://github.com/scikit-image/scikit-image/pull/7459>_).
Remove unused and deprecated dependency pytest-runner (#7495 <https://github.com/scikit-image/scikit-image/pull/7495>_).
Exclude imageio 2.35.0 that forces numpy downgrade (#7502 <https://github.com/scikit-image/scikit-image/pull/7502>_).
Don't test thresholding funcs for Dask compatibility (#7509 <https://github.com/scikit-image/scikit-image/pull/7509>_).
Fix build dependency (#7510 <https://github.com/scikit-image/scikit-image/pull/7510>_).
Add sdist check to spin sdist (#7438 <https://github.com/scikit-image/scikit-image/pull/7438>_).
Reorder items in TODO list (#7519 <https://github.com/scikit-image/scikit-image/pull/7519>_).
Use Rotation.from_euler to compute 3D rotation matrix (#7503 <https://github.com/scikit-image/scikit-image/pull/7503>_).
Update spin (0.12) (#7532 <https://github.com/scikit-image/scikit-image/pull/7532>_).
Import lazy_loader as private symbol in top-level namespaces (#7540 <https://github.com/scikit-image/scikit-image/pull/7540>_).
Set -DNPY_NO_DEPRECATED_API=NPY_1_23_API_VERSION on build (#7538 <https://github.com/scikit-image/scikit-image/pull/7538>_).
Update up/download artifact version (#7545 <https://github.com/scikit-image/scikit-image/pull/7545>_).
Don't use deprecated io.show and io.imshow (#7556 <https://github.com/scikit-image/scikit-image/pull/7556>_).
Hide traceback inside assert_stacklevel (#7558 <https://github.com/scikit-image/scikit-image/pull/7558>_).
Update pre-commit versions (#7560 <https://github.com/scikit-image/scikit-image/pull/7560>_).
Drop Python 3.9 support (#7561 <https://github.com/scikit-image/scikit-image/pull/7561>_).
Update minimum dependencies (SPEC 0) (#7562 <https://github.com/scikit-image/scikit-image/pull/7562>_).
Remove unused PYX files in io/plugins (#7557 <https://github.com/scikit-image/scikit-image/pull/7557>).
Support Python 3.13 (#7565 <https://github.com/scikit-image/scikit-image/pull/7565>_).
During deprecation cycles, preserve the value of deprecated parameters that don't have a new parameter as a replacement (#7552 <https://github.com/scikit-image/scikit-image/pull/7552>_).
Fix missing minigalleries by using full names in directives (#7567 <https://github.com/scikit-image/scikit-image/pull/7567>_).
Build Python 3.13 wheels (#7571 <https://github.com/scikit-image/scikit-image/pull/7571>_).
Update TODO (#7573 <https://github.com/scikit-image/scikit-image/pull/7573>_).
Remove deprecated gaussian output parameter (#7574 <https://github.com/scikit-image/scikit-image/pull/7574>_).
Test Py3.13 on windows (#7578 <https://github.com/scikit-image/scikit-image/pull/7578>_).
Update ruff linter / formatter (#7580 <https://github.com/scikit-image/scikit-image/pull/7580>_).
Fix formatting issues (#7581 <https://github.com/scikit-image/scikit-image/pull/7581>_).
CI: bump macos image pin from 12 to 13 (#7582 <https://github.com/scikit-image/scikit-image/pull/7582>_).
Update build dependencies (#7587 <https://github.com/scikit-image/scikit-image/pull/7587>_).
Update minimum supported pyamg (#7586 <https://github.com/scikit-image/scikit-image/pull/7586>_).
Update documentation dependencies (#7590 <https://github.com/scikit-image/scikit-image/pull/7590>_).
Bump changelist to v0.5 (#7601 <https://github.com/scikit-image/scikit-image/pull/7601>_).
Pin kaleido to 0.2.1 (#7612 <https://github.com/scikit-image/scikit-image/pull/7612>_).
Update upload-nightly-action (#7609 <https://github.com/scikit-image/scikit-image/pull/7609>_).
Update pillow (#7615 <https://github.com/scikit-image/scikit-image/pull/7615>_).
Remove Python 2.7 cruft (#7616 <https://github.com/scikit-image/scikit-image/pull/7616>_).
Use intersphinx_registry package in conf.py to keep intersphinx urls up to date. This means that building docs now requires the intersphinx-registry package (#7611 <https://github.com/scikit-image/scikit-image/pull/7611>_).
Update build dependencies (#7614 <https://github.com/scikit-image/scikit-image/pull/7614>_).
Update file extension and reformat Markdown file (#7617 <https://github.com/scikit-image/scikit-image/pull/7617>_).
Add forgotten TODO about deprecated square, cube & rectangle (#7624 <https://github.com/scikit-image/scikit-image/pull/7624>_).
Upgrade to spin 0.13 (#7622 <https://github.com/scikit-image/scikit-image/pull/7622>_).
Lazy load legacy imports in skimage top module (#6892 <https://github.com/scikit-image/scikit-image/pull/6892>_).
CI pre-commit fix (#7631 <https://github.com/scikit-image/scikit-image/pull/7631>_).

Contributors

30 authors added to this release (alphabetically):

@aeisenbarth <https://github.com/aeisenbarth>_
@FedericoWZhaw <https://github.com/FedericoWZhaw>_
@jakirkham <https://github.com/jakirkham>_
@michaelbratsch <https://github.com/michaelbratsch>_
Adeyemi Biola (@decorouz <https://github.com/decorouz>_)
Aditi Juneja (@Schefflera-Arboricola <https://github.com/Schefflera-Arboricola>_)
Agriya Khetarpal (@agriyakhetarpal <https://github.com/agriyakhetarpal>_)
Brigitta Sipőcz (@bsipocz <https://github.com/bsipocz>_)
Dan Schult (@dschult <https://github.com/dschult>_)
Edgar Andrés Margffoy Tuay (@andfoy <https://github.com/andfoy>_)
Egor Panfilov (@soupault <https://github.com/soupault>_)
Erik Welch (@eriknw <https://github.com/eriknw>_)
Gianluca (@geeanlooca <https://github.com/geeanlooca>_)
Gregory Lee (@grlee77 <https://github.com/grlee77>_)
Hayato Ikoma (@hayatoikoma <https://github.com/hayatoikoma>_)
Henrik Finsberg (@finsberg <https://github.com/finsberg>_)
Jarrod Millman (@jarrodmillman <https://github.com/jarrodmillman>_)
Jordão Bragantini (@JoOkuma <https://github.com/JoOkuma>_)
João Seródio (@SerodioJ <https://github.com/SerodioJ>_)
Kushaan Gupta (@kushaangupta <https://github.com/kushaangupta>_)
Lars Grüter (@lagru <https://github.com/lagru>_)
Loïc Estève (@lesteve <https://github.com/lesteve>_)
M Bussonnier (@Carreau <https://github.com/Carreau>_)
Marianne Corvellec (@mkcor <https://github.com/mkcor>_)
Mark Harfouche (@hmaarrfk <https://github.com/hmaarrfk>_)
Matthew Feickert (@matthewfeickert <https://github.com/matthewfeickert>_)
Paritosh Dahiya (@hnhparitosh <https://github.com/hnhparitosh>_)
Piyush Amitabh (@pamitabh <https://github.com/pamitabh>_)
Ricky Walsh (@rickymwalsh <https://github.com/rickymwalsh>_)
Stefan van der Walt (@stefanv <https://github.com/stefanv>_)

25 reviewers added to this release (alphabetically):

@aeisenbarth <https://github.com/aeisenbarth>_
@FedericoWZhaw <https://github.com/FedericoWZhaw>_
@jakirkham <https://github.com/jakirkham>_
@michaelbratsch <https://github.com/michaelbratsch>_
Agriya Khetarpal (@agriyakhetarpal <https://github.com/agriyakhetarpal>_)
Brigitta Sipőcz (@bsipocz <https://github.com/bsipocz>_)
Dan Schult (@dschult <https://github.com/dschult>_)
Edgar Andrés Margffoy Tuay (@andfoy <https://github.com/andfoy>_)
Egor Panfilov (@soupault <https://github.com/soupault>_)
Gianluca (@geeanlooca <https://github.com/geeanlooca>_)
Gregory Lee (@grlee77 <https://github.com/grlee77>_)
Hayato Ikoma (@hayatoikoma <https://github.com/hayatoikoma>_)
Jarrod Millman (@jarrodmillman <https://github.com/jarrodmillman>_)
Jordão Bragantini (@JoOkuma <https://github.com/JoOkuma>_)
João Seródio (@SerodioJ <https://github.com/SerodioJ>_)
Juan Nunez-Iglesias (@jni <https://github.com/jni>_)
Kushaan Gupta (@kushaangupta <https://github.com/kushaangupta>_)
Lars Grüter (@lagru <https://github.com/lagru>_)
Marianne Corvellec (@mkcor <https://github.com/mkcor>_)
Mark Harfouche (@hmaarrfk <https://github.com/hmaarrfk>_)
Matthew Feickert (@matthewfeickert <https://github.com/matthewfeickert>_)
Nathan Goldbaum (@ngoldbaum <https://github.com/ngoldbaum>_)
Piyush Amitabh (@pamitabh <https://github.com/pamitabh>_)
Ralf Gommers (@rgommers <https://github.com/rgommers>_)
Stefan van der Walt (@stefanv <https://github.com/stefanv>_)

These lists are automatically generated, and may not be complete or may contain duplicates.