v0.25.0

scikit-image 0.25.0

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).
• Add the new skimage.morphology.footprint_rectangle supporting generation of rectangular or hyper-rectangular footprints in one function (#7566).

API Changes

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

Enhancements

• Improve numerical stability of skimage.morphology.local_minima for extremely small floats (#7534).
• Make sure that skimage.feature.plot_matched_features uses the same random colors, if matches_color isn't provided explicitly (#7541).
• Allow passing a sequence of colors to the parameter matches_color in skimage.feature.plot_matched_features (#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).
• In skimage.featurepeak_local_max, skip unnecessary check for cases where min_distance > 1 is passed (#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).
• Fix degeneracy in skimage.draw.ellipsoid_stats when all semi-axes have the same length (#7473).
• Prevent skimage.morphology.thin from accidentally modifying the input image in case it is of dtype uint8 (#7469).
• Fix numerical precision error in skimage.measure.ransac. In some cases, ransac was stopping at the first iteration (#7065).
• Fix numerical precision error in skimage.measure.ransac; very small probabilities lead to -0 number of max trials (#7496).
• Ensure that RegionProperties objects returned by skimage.measure.regionprops can be deserialized with pickle (#7569).
• Fix edge case where setting watershed_lines=True in skimage.segmentation.watershed resulted in an incorrect solution (#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).
• Fix dtype promotion in skimage.segmentation.join_segmentations if numpy.uint is used with NumPy<2 (#7292).

Documentation

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

Infrastructure

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

Maintenance

• Verify all artifacts that have been attested by looping over them in CI (#7447).
• Update circleci-artifacts-redirector-action that moved to the Scientific Python org (#7446).
• Use NumPy 2.0 stable to build packages (#7451).
• FIX Use python3 in Meson version script shebang (#7482).
• Refactored tests for skeletonize (#7459).
• Remove unused and deprecated dependency pytest-runner (#7495).
• Exclude imageio 2.35.0 that forces numpy downgrade (#7502).
• Don't test thresholding funcs for Dask compatibility (#7509).
• Fix build dependency (#7510).
• Add sdist check to spin sdist (#7438).
• Reorder items in TODO list (#7519).
• Use Rotation.from_euler to compute 3D rotation matrix (#7503).
• Update spin (0.12) (#7532).
• Import lazy_loader as private symbol in top-level namespaces ([#7540](https://github.com/scikit-image/scikit...

v0.25.0rc2

scikit-image 0.25.0rc2

We're happy to announce the release of scikit-image 0.25.0rc2!

New Features

• Add the new Gray-Level Co-occurrence Matrix (GLCM) properties "mean", "variance", "standard deviation" and "entropy" to skimage.feature.texture.graycoprops (#7375).
• Add the new skimage.morphology.footprint_rectangle supporting generation of rectangular or hyper-rectangular footprints in one function (#7566).

API Changes

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

Enhancements

• Improve numerical stability of skimage.morphology.local_minima for extremely small floats (#7534).
• Allow passing a sequence of colors to the parameter matches_color in skimage.feature.plot_matched_features (#7541).
• Make sure that skimage.feature.plot_matched_features uses the same random colors, if matches_color isn't provided explicitly (#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).
• In skimage.featurepeak_local_max, skip unnecessary check for cases where min_distance > 1 is passed (#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).
• Fix degeneracy in skimage.draw.ellipsoid_stats when all semi-axes have the same length (#7473).
• Prevent skimage.morphology.thin from accidentally modifying the input image in case it is of dtype uint8 (#7469).
• Fix numerical precision error in skimage.measure.ransac. In some cases, ransac was stopping at the first iteration (#7065).
• Fix numerical precision error in skimage.measure.ransac; very small probabilities lead to -0 number of max trials (#7496).
• Ensure that RegionProperties objects returned by skimage.measure.regionprops can be deserialized with pickle (#7569).
• 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).
• Fix edge case where setting watershed_lines=True in skimage.segmentation.watershed resulted in an incorrect solution (#7071).
• Fix dtype promotion in skimage.segmentation.join_segmentations if numpy.uint is used with NumPy<2 (#7292).

Documentation

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

Infrastructure

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

Maintenance

• Verify all artifacts that have been attested by looping over them in CI (#7447).
• Update circleci-artifacts-redirector-action that moved to the Scientific Python org (#7446).
• Use NumPy 2.0 stable to build packages (#7451).
• FIX Use python3 in Meson version script shebang (#7482).
• Refactored tests for skeletonize (#7459).
• Remove unused and deprecated dependency pytest-runner (#7495).
• Exclude imageio 2.35.0 that forces numpy downgrade (#7502).
• Don't test thresholding funcs for Dask compatibility (#7509).
• Fix build dependency (#7510).
• Add sdist check to spin sdist (#7438).
• Reorder items in TODO list (#7519).
• Use Rotation.from_euler to compute 3D rotation matrix (#7503).
• Update spin (0.12) (#7532).
• Import lazy_loader as private symbol in top-level namespaces ([#7540](https://github.com/scikit-image/...

v0.25.0rc1

scikit-image 0.25.0rc1

We're happy to announce the release of scikit-image 0.25.0rc1!

New Features

• Add the new Grey-Level Co-occurrence Matrix (GLCM) properties "mean", "variance", "standard deviation" and "entropy" to skimage.feature.texture.graycoprops (#7375).

API Changes

• Complete the deprecation of and remove skimage.feature.plot_matches. Use skimage.feature.plot_matched_features going forward (#7487).
• Deprecate skimage.io.imshow, skimage.io.imshow_collection and skimage.io.show. Please use matplotlib, napari, etc. to visualize images (#7508).

Enhancements

• Improve numerical stability of skimage.morphology.local_minima for extremely small floats (#7534).

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).
• Fix degeneracy in skimage.draw.ellipsoid_stats when all semi-axes have the same length (#7473).
• Prevent skimage.morphology.thin from accidentally modifying the input image in case it is of dtype uint8 (#7469).
• Fix numerical precision error in skimage.measure.ransac. In some cases, ransac was stopping at the first iteration (#7065).
• Fix numerical precision error in skimage.measure.ransac; very small probabilities lead to -0 number of max trials (#7496).

Documentation

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

Infrastructure

• Fix CI tests with minimal dependencies and make dependency resolution more robust (#7462).
• Add CI to test scikit-image against free-threaded Python 3.13 (#7463).
• Address autosummary.import_cycle warning (#7486).
• Temporarily exclude Dask 2024.8.0 to fix CI (#7493).
• Uncomment currentmodule directive again (#7492).
• Add CI to release nightly free-threaded wheels (#7481).
• Update deprecated configuration (#7501).
• Bump spin version to 0.11 (#7507).
• Ensure only a single type: label is present in PRs (#7512).
• Update pydata-sphinx-theme (#7511).
• Fix OpenBLAS s_cmp unresolved symbol error, update Emscripten CI testing (#7525).

Maintenance

• Verify all artifacts that have been attested by looping over them in CI (#7447).
• Update circleci-artifacts-redirector-action that moved to the Scientific Python org (#7446).
• Use NumPy 2.0 stable to build packages (#7451).
• FIX Use python3 in Meson version script shebang (#7482).
• Refactored tests for skeletonize (#7459).
• Remove unused and deprecated dependency pytest-runner (#7495).
• Exclude imageio 2.35.0 that forces numpy downgrade (#7502).
• Don't test thresholding funcs for Dask compatibility (#7509).
• Fix build dependency (#7510).
• Add sdist check to spin sdist (#7438).
• Reorder items in TODO list (#7519).
• Use Rotation.from_euler to compute 3D rotation matrix (#7503).
• Update spin (0.12) (#7532).
• Import lazy_loader as private symbol in top-level namespaces (#7540).
• Set -DNPY_NO_DEPRECATED_API=NPY_1_23_API_VERSION on build (#7538).
• Update up/download artifact version (#7545).
• Don't use deprecated io.show and io.imshow (#7556).
• Hide traceback inside assert_stacklevel (#7558).
• Update pre-commit versions (#7560).
• Drop Python 3.9 support (#7561).
• Update minimum dependencies (SPEC 0) (#7562).
• Remove unused PYX files in io/_plugins (#7557).
• Support Python 3.13 (#7565).
• During deprecation cycles, preserve the value of deprecated parameters that don't have a new parameter as a replacement (#7552).
• Fix missing minigalleries by using full names in directives (#7567).
• Build Python 3.13 wheels (#7571).
• Update TODO (#7573).
• Remove deprecated skeletonize_3d (#7572).
• Remove deprecated gaussian output parameter (#7574).

Contributors

21 authors added to this release (alphabetically):

• @FedericoWZhaw
• @jakirkham
• @michaelbratsch
• Adeyemi Biola (@decorouz)
• Agriya Khetarpal (@agriyakhetarpal)
• Brigitta Sipőcz (@bsipocz)
• Edgar Andrés Margffoy Tuay (@andfoy)
• Egor Panfilov (@soupault)
• Erik Welch (@eriknw)
• Gianluca (@geeanlooca)
• Hayato Ikoma (@hayatoikoma)
• Jarrod Millman (@jarrodmillman)
• João Seródio (@SerodioJ)
• Kushaan Gupta (@kushaangupta)
• Lars Grüter (@lagru)
• Loïc Estève (@lesteve)
• Marianne Corvellec (@mkcor)
• Mark Harfouche (@hmaarrfk)
• Matthew Feickert (@matthewfeickert)
• Piyush Amitabh (@pamitabh)
• Stefan van der Walt (@stefanv)

20 reviewers added to this release (alphabetically):

• @FedericoWZhaw
• @jakirkham
• @michaelbratsch
• Agriya Khetarpal (@agriyakhetarpal)
• Brigitta Sipőcz (@bsipocz)
• Edgar Andrés Margffoy Tuay (@andfoy)
• Egor Panfilov (@soupault)
• Gianluca (@geeanlooca)
• Hayato Ikoma (@hayatoikoma)
• Jarrod Millman (@jarrodmillman)
• João Seródio ([@serod...

v0.25.0rc0

signed 0.25.0rc0 tag

v0.24.0

scikit-image 0.24.0

We're happy to announce the release of scikit-image 0.24.0!

Highlights

• Add new class skimage.transform.ThinPlateSplineTransform, which can estimate and model non-linear transforms with thin-plate splines and allows image warping with skimage.transform.warp (#7040).

New Features

• Add new class skimage.transform.ThinPlateSplineTransform, which can estimate and model non-linear transforms with thin-plate splines and allows image warping with skimage.transform.warp (#7040).
• Add skimage.morphology.remove_objects_by_distance, which removes labeled objects, ordered by size (default), until the remaining objects are a given distance apart (#4165).

Performance

• In skimage.feature.corner_fast, test four directions earlier, which should more than half the computation time for most cases (#7394).

Documentation

• Remove obsolete instruction about documenting changes (#7321).
• Clarify description of data_range parameter in skimage.metrics.structural_similarity (#7345).
• Update release process notes (#7402).
• Fix typo in docstring of skimage.measure.regionprops (#7405).
• Fix typos in skimage.measure.find_contours (#7411).
• Add algorithmic complexity description + suggested alternatives to skimage.restoration.rolling_ball docstring (#7424).
• Remove ineffective PR contribution clause (#7429).
• Clarify objection period for lazy consensus in SKIP 1 (#7020).
• Add a new gallery example "Use thin-plate splines for image warping" (#7040).
• Add a new gallery example on "Removing objects" based on their size or distance (#4165).

Infrastructure

• Escape user-controlled variables in GA workflow (#7415).
• Add generation of GitHub artifact attestations to built sdist and wheels before upload to PyPI (#7427).
• For publishing actions use the full length commit SHA (#7433).
• Be mindful of resources by canceling in-progress workflows (#7436).
• Add out-of-tree Pyodide builds in CI for scikit-image (#7350).

Maintenance

• Replace deprecated nose style setup/teardown with autouse fixtures (#7343).
• Temporarily pin macos-12 runner in CI (#7408).
• Fix NumPy2 dtype promotion issues in pywt dependent code (#7414).
• In skimage.util.compare_images, deprecate the parameter image2. Instead use image0, image1 to pass the compared images. Furthermore, all other parameters will be turned into keyword-only parameters once the deprecation is complete (#7322).
• Add support back for Python 3.9 to enhance compatibility with Numpy 2 (#7412).
• Disable ruff/pyupgrade rule UP038 (#7430).
• Stop verifying wheel attestations temporarily (#7444).

Contributors

13 authors added to this release (alphabetically):

• Adeyemi Biola (@decorouz)
• Agriya Khetarpal (@agriyakhetarpal)
• Ananya Srivastava (@ana42742)
• Curtis Rueden (@ctrueden)
• Jarrod Millman (@jarrodmillman)
• Juan Nunez-Iglesias (@jni)
• Lars Grüter (@lagru)
• Marianne Corvellec (@mkcor)
• Mark Harfouche (@hmaarrfk)
• Matthew Feickert (@matthewfeickert)
• Pang (@lartpang)
• Stefan van der Walt (@stefanv)
• 武士风度的牛 (@spdfghi)

15 reviewers added to this release (alphabetically):

• Adeyemi Biola (@decorouz)
• Agriya Khetarpal (@agriyakhetarpal)
• Curtis Rueden (@ctrueden)
• Egor Panfilov (@soupault)
• Jarrod Millman (@jarrodmillman)
• Juan Nunez-Iglesias (@jni)
• Lars Grüter (@lagru)
• Marianne Corvellec (@mkcor)
• Mark Harfouche (@hmaarrfk)
• Matthew Feickert (@matthewfeickert)
• Ralf Gommers (@rgommers)
• Riadh Fezzani (@rfezzani)
• Sebastian Berg (@seberg)
• Stefan van der Walt (@stefanv)
• Tyler Reddy (@tylerjereddy)

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

v0.24.0rc1

scikit-image 0.24.0rc1

We're happy to announce the release of scikit-image 0.24.0rc1!

Highlights

• Add new class skimage.transform.ThinPlateSplineTransform, which can estimate and model non-linear transforms with thin-plate splines and allows image warping with skimage.transform.warp (#7040).

New Features

• Add new class skimage.transform.ThinPlateSplineTransform, which can estimate and model non-linear transforms with thin-plate splines and allows image warping with skimage.transform.warp (#7040).
• Add skimage.morphology.remove_objects_by_distance, which removes labeled objects, ordered by size (default), until the remaining objects are a given distance apart (#4165).

Performance

• In skimage.feature.corner_fast, test four directions earlier, which should more than half the computation time for most cases (#7394).

Documentation

• Remove obsolete instruction about documenting changes (#7321).
• Clarify description of data_range parameter in skimage.metrics.structural_similarity (#7345).
• Update release process notes (#7402).
• Fix typo in docstring of skimage.measure.regionprops (#7405).
• Fix typos in skimage.measure.find_contours (#7411).
• Add algorithmic complexity description + suggested alternatives to skimage.restoration.rolling_ball docstring (#7424).
• Remove ineffective PR contribution clause (#7429).
• Clarify objection period for lazy consensus in SKIP 1 (#7020).
• Add a new gallery example "Use thin-plate splines for image warping" (#7040).
• Add a new gallery example on "Removing objects" based on their size or distance (#4165).

Infrastructure

• Escape user-controlled variables in GA workflow (#7415).
• Add generation of GitHub artifact attestations to built sdist and wheels before upload to PyPI (#7427).
• For publishing actions use the full length commit SHA (#7433).
• Be mindful of resources by canceling in-progress workflows (#7436).
• Add out-of-tree Pyodide builds in CI for scikit-image (#7350).

Maintenance

• Replace deprecated nose style setup/teardown with autouse fixtures (#7343).
• Temporarily pin macos-12 runner in CI (#7408).
• Fix NumPy2 dtype promotion issues in pywt dependent code (#7414).
• In skimage.util.compare_images, deprecate the parameter image2. Instead use image0, image1 to pass the compared images. Furthermore, all other parameters will be turned into keyword-only parameters once the deprecation is complete (#7322).
• Add support back for Python 3.9 to enhance compatibility with Numpy 2 (#7412).
• Disable ruff/pyupgrade rule UP038 (#7430).

Contributors

13 authors added to this release (alphabetically):

• Adeyemi Biola (@decorouz)
• Agriya Khetarpal (@agriyakhetarpal)
• Ananya Srivastava (@ana42742)
• Curtis Rueden (@ctrueden)
• Jarrod Millman (@jarrodmillman)
• Juan Nunez-Iglesias (@jni)
• Lars Grüter (@lagru)
• Marianne Corvellec (@mkcor)
• Mark Harfouche (@hmaarrfk)
• Matthew Feickert (@matthewfeickert)
• Pang (@lartpang)
• Stefan van der Walt (@stefanv)
• 武士风度的牛 (@spdfghi)

15 reviewers added to this release (alphabetically):

• Adeyemi Biola (@decorouz)
• Agriya Khetarpal (@agriyakhetarpal)
• Curtis Rueden (@ctrueden)
• Egor Panfilov (@soupault)
• Jarrod Millman (@jarrodmillman)
• Juan Nunez-Iglesias (@jni)
• Lars Grüter (@lagru)
• Marianne Corvellec (@mkcor)
• Mark Harfouche (@hmaarrfk)
• Matthew Feickert (@matthewfeickert)
• Ralf Gommers (@rgommers)
• Riadh Fezzani (@rfezzani)
• Sebastian Berg (@seberg)
• Stefan van der Walt (@stefanv)
• Tyler Reddy (@tylerjereddy)

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

v0.24.0rc0

scikit-image 0.24.0rc0

We're happy to announce the release of scikit-image 0.24.0rc0!

Highlights

• Add new class skimage.transform.ThinPlateSplineTransform, which can estimate and model non-linear transforms with thin-plate splines and allows image warping with skimage.transform.warp (#7040).

New Features

• Add new class skimage.transform.ThinPlateSplineTransform, which can estimate and model non-linear transforms with thin-plate splines and allows image warping with skimage.transform.warp (#7040).
• Add skimage.morphology.remove_objects_by_distance, which removes labeled objects, ordered by size (default), until the remaining objects are a given distance apart (#4165).

Performance

• In skimage.feature.corner_fast, test four directions earlier, which should more than half the computation time for most cases (#7394).

Documentation

• Remove obsolete instruction about documenting changes (#7321).
• Clarify description of data_range parameter in skimage.metrics.structural_similarity (#7345).
• Update release process notes (#7402).
• Fix typo in docstring of skimage.measure.regionprops (#7405).
• Fix typos in skimage.measure.find_contours (#7411).
• Add algorithmic complexity description + suggested alternatives to skimage.restoration.rolling_ball docstring (#7424).
• Remove ineffective PR contribution clause (#7429).
• Clarify objection period for lazy consensus in SKIP 1 (#7020).
• Add a new gallery example "Use thin-plate splines for image warping" (#7040).
• Add a new gallery example on "Removing objects" based on their size or distance (#4165).

Infrastructure

• Escape user-controlled variables in GA workflow (#7415).
• Add generation of GitHub artifact attestations to built sdist and wheels before upload to PyPI (#7427).
• For publishing actions use the full length commit SHA (#7433).
• Be mindful of resources by canceling in-progress workflows (#7436).
• Add out-of-tree Pyodide builds in CI for scikit-image (#7350).

Maintenance

• Replace deprecated nose style setup/teardown with autouse fixtures (#7343).
• Temporarily pin macos-12 runner in CI (#7408).
• Fix NumPy2 dtype promotion issues in pywt dependent code (#7414).
• In skimage.util.compare_images, deprecate the parameter image2. Instead use image0, image1 to pass the compared images. Furthermore, all other parameters will be turned into keyword-only parameters once the deprecation is complete (#7322).
• Add support back for Python 3.9 to enhance compatibility with Numpy 2 (#7412).
• Disable ruff/pyupgrade rule UP038 (#7430).

Contributors

13 authors added to this release (alphabetically):

• Adeyemi Biola (@decorouz)
• Agriya Khetarpal (@agriyakhetarpal)
• Ananya Srivastava (@ana42742)
• Curtis Rueden (@ctrueden)
• Jarrod Millman (@jarrodmillman)
• Juan Nunez-Iglesias (@jni)
• Lars Grüter (@lagru)
• Marianne Corvellec (@mkcor)
• Mark Harfouche (@hmaarrfk)
• Matthew Feickert (@matthewfeickert)
• Pang (@lartpang)
• Stefan van der Walt (@stefanv)
• 武士风度的牛 (@spdfghi)

15 reviewers added to this release (alphabetically):

• Adeyemi Biola (@decorouz)
• Agriya Khetarpal (@agriyakhetarpal)
• Curtis Rueden (@ctrueden)
• Egor Panfilov (@soupault)
• Jarrod Millman (@jarrodmillman)
• Juan Nunez-Iglesias (@jni)
• Lars Grüter (@lagru)
• Marianne Corvellec (@mkcor)
• Mark Harfouche (@hmaarrfk)
• Matthew Feickert (@matthewfeickert)
• Ralf Gommers (@rgommers)
• Riadh Fezzani (@rfezzani)
• Sebastian Berg (@seberg)
• Stefan van der Walt (@stefanv)
• Tyler Reddy (@tylerjereddy)

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

v0.23.2

scikit-image 0.23.2

We're happy to announce the release of scikit-image 0.23.2!

Bug Fixes

• Make sure skimage.util.img_as_ubyte supports the edge case where dtype('uint64').type of the provided image is np.ulonglong instead of np.uint64 (#7392).

Documentation

• Add date to 0.23.1 release notes (#7384).
• Fix docstring of connectivity parameter in skimage.segmentation.watershed (#7360).

Infrastructure

• Ignore Sphinx warning about unpickable cache (#7400).
• Simplify instructions on changelist in PR template (#7401).

Maintenance

• Use numpy.inf instead of deprecated numpy.infty (#7386).
• Update Ruff config (#7387).
• Update matrix and names of Azure pipelines configuration (#7390).
• Use upload- and download-artifact v4 (#7389).
• Ignore arch specific cast warnings originating from astype in tests (#7393).
• Update link to numpydoc example.py (#7395).

Contributors

4 authors added to this release (alphabetically):

• @pitkajuh
• Jarrod Millman (@jarrodmillman)
• Lars Grüter (@lagru)
• Marianne Corvellec (@mkcor)

4 reviewers added to this release (alphabetically):

• Egor Panfilov (@soupault)
• Jarrod Millman (@jarrodmillman)
• Lars Grüter (@lagru)
• Marianne Corvellec (@mkcor)

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

v0.23.2rc1

scikit-image 0.23.2rc1

Important

This is a release candidate for a minor patch release!

We're happy to announce the release of scikit-image 0.23.2rc1!

Bug Fixes

• Make sure skimage.util.img_as_ubyte supports the edge case where dtype('uint64').type of the provided image is np.ulonglong instead of np.uint64 (#7392).

Documentation

• Add date to 0.23.1 release notes (#7384).
• Fix docstring of connectivity parameter in skimage.segmentation.watershed (#7360).

Maintenance

• Use numpy.inf instead of deprecated numpy.infty (#7386).
• Update Ruff config (#7387).
• Update matrix and names of Azure pipelines configuration (#7390).
• Use upload- and download-artifact v4 (#7389).
• Ignore arch specific cast warnings originating from astype in tests (#7393).
• Update link to numpydoc example.py (#7395).

Contributors

4 authors added to this release (alphabetically):

• @pitkajuh
• Jarrod Millman (@jarrodmillman)
• Lars Grüter (@lagru)
• Marianne Corvellec (@mkcor)

3 reviewers added to this release (alphabetically):

• Egor Panfilov (@soupault)
• Jarrod Millman (@jarrodmillman)
• Lars Grüter (@lagru)

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

v0.23.1

scikit-image 0.23.1

We're happy to announce the release of scikit-image 0.23.1!

Note

Due to an issue with the CI system scikit-image 0.23.0 was never released.
This release is identical to what 0.23.0 would have been other than the CI fix and the version number.

Highlights

• Ensure skimage.morphology.closing and skimage.morphology.opening are extensive and anti-extensive, respectively, if the footprint is not mirror symmetric (#6695).
• Add parameter mode to binary_erosion, binary_dilation, binary_opening and binary_closing in skimage.morphology. These new parameters determine how array borders are handled (#6695).
• Add parameters mode and cval to erosion, dilation, opening, closing, white_tophat, and black_tophat in skimage.morphology. These new parameters determine how array borders are handled (#6695).
• Speedup skimage.util.map_array by parallelization with Cython's prange (#7266).

New Features

• Add new intensity_std property to skimage.measure.regionprops which computes the standard deviation of the intensity in a region (#6712).
• Add parameter mode to binary_erosion, binary_dilation, binary_opening and binary_closing in skimage.morphology. These new parameters determine how array borders are handled (#6695).
• Add functions mirror_footprint and pad_footprint to skimage.morphology (#6695).
• Add parameters mode and cval to erosion, dilation, opening, closing, white_tophat, and black_tophat in skimage.morphology. These new parameters determine how array borders are handled (#6695).
• Add new parameter spacing to segmentation.expand_labels to support anisotropic images (#7080).

API Changes

• Drop support for Python 3.9 (#7217).
• Parameters shift_x and shift_y in skimage.morphology.erosion and skimage.morphology.dilation are deprecated. Use pad_footprint or modify the footprint manually instead (#6695).
• Remove unexpected value scaling in skimage.morphology.skeletonize_3d for non-binary input images. skeletonize_3d now always returns a binary array like similar functions (#7095).
• Deprecate function skimage.feature.plot_matches in favor of skimage.feature.plot_matched_features (#7255).
• Deprecate skimage.morphology.skeletonize_3d in favor of just skimage.morphology.skeletonize (#7094).
• Deprecate parameter output in skimage.filters.gaussian; use out instead (#7225).
• Change the default value of the parameters shift_x, shift_y and shift_z from False to 0 in the skimage.filters.rank functions. This has not impact on the results. Warn in case boolean shifts are provided from now on (#7320).

Performance

• Add lazy loading to skimage.metrics module (#7211).
• Speedup skimage.util.map_array by parallelization with Cython's prange (#7266).

Bug Fixes

• Add exception to avoid surprising result when image is too small for the given parameters in skimage.feature.hog (#7153).
• Ensure skimage.morphology.closing and skimage.morphology.opening are extensive and anti-extensive, respectively, if the footprint is not mirror symmetric (#6695).
• Avoid a TypeError in skimage.registration.phase_cross_correlation when the real-time shift cannot be determined (disambiguate=True). Display a warning instead (#7259).
• Fix logic in skimage.graph.pixel_graph which raised a TypeError when the parameter edge_function was provided without a mask (#7310).
• Ensure cache stays empty when cache=False is passed to skimage.measure.regionprops (#7333).

Documentation

• Update instructions for updating dev environment (#7160).
• Make titles in RAG gallery examples more explicit (#7202).
• Add docstring to skimage.graph module (#7192).
• Use consistent notation for array dimensions in the docstrings (#3031).
• Specify default markers in watershed docstring (#7154).
• Stop HTML documentation from intercepting left and right-arrow keys to improve keyboard accessibility (#7226).
• Fix reference formatting for nitpicky sphinx (#7228).
• Document how to deal with other array-likes such as xarray.DataArray and pandas.DataFrame in the crash course on NumPy for images (#7159).
• Fix broken function calls and syntax issues in user guide (#7234).
• Use correct default mode in docstring of skimage.transform.swirl (#7241).
• Add missing documentation about spacing parameter in moments_normalized (#7248).
• Update docstring & example in the hough_ellipse transform (#6893).
• Point binder tag/branch to commit corresponding to docs/release (#7252).
• Add example to FundamentalMatrixTransform class (#6863).
• Adds explanation of what the optional dependency on Matplotlib offers to the install instructions (#7286).
• Use correct symbol θ for tightness in the docstring of skimage.registration.optical_flow_tvl1 (#7314).
• The description of the parameter cval is modified in "int or float". cval is a numerical value not a string (#7319).
• Remove obsolete instruction about documenting changes (#7321).
• Added comment to clarify that dt corresponds to tau, i.e. the time step. Changed gray scale in grayscale in the entire registration module (#7324).
• Create SECURITY.md (#7230).
• Remove deprecated parameter coordinates from docstring example of skimage.segmentation.active_contour (#7329).
• Include dates in release note headings (#7269).
• Update description of how to document pull requests for inclusion in the release notes (#7267).
• Clarify description of data_range parameter in skimage.metrics.structural_similarity (#7345).
• Use object-oriented Matplotlib style in longer gallery examples and demonstrations (doc/examples/applications) (#7346).
• In the gallery example on segmenting human cells (in mitosis), include the border when generating basin markers for watershed (#7362).
• Add missing minus sign in docstring of skimage.transform.EuclideanTransform (#7097).

Infrastructure

• Update wording on the stale bot to assume the core team dropped the ball (#7196).
• Update Azure job name following the drop of Python 3.9 (#7218).
• Schedule nightly wheel builds at uncommon time (#7254).
• Build nightly wheels with nightly NumPy 2.0 (#7251).
• Use pytest-doctestplus instead of classic pytest-doctest (#7289).
• Update the scientific-python/upload-nightly-action to v0.5.0 for dependency stability and to take advantage of Anaconda Cloud upload bug fixes (#7325).
• Add assert_stacklevel helper to check stacklevel of captured warnings (#7294).
• Exclude pre-commit[bot] from changelist's contributor list ([#735...