scikit-image 0.19.3 (2022-06-12)#

We’re happy to announce the release of scikit-image v0.19.3!

scikit-image is an image processing toolbox for SciPy that includes algorithms for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more.

For more information, examples, and documentation, please visit our website:

https://scikit-image.org

Bugs Fixed#

  • Revert unintentional change to default multichannel behavior introduced in v0.19.0 for skimage.restoration.cycle_spin (now defaults to single channel again)

  • Fix corner case with an optimal angle of 0 degrees in hough_line_peaks

  • Fixed the gallery example involving registration with log-polar transformations

  • Update test suite for compatibility with the most recent tifffile release.

  • warp/rotate: fixed a bug with clipping when cval is not in the input range

  • Fix computation of histogram bins for multichannel integer-valued images

General Maintenance#

  • Update skimage.future.manual_polygon_segmentation to work with Matplotlib 3.5.

  • Update skimage.io.imread to avoid warnings when using imageio>=2.16.2.

  • Now compatible with Pillow >= 9.1 (palette may contain <256 entries)

  • Added support for NumPy 1.23

Pull Requests Included#

  • Backport PR #6306 on branch v0.19.x (Fix for error in ‘Using Polar and Log-Polar Transformations for Registration’) (#6312)

  • Backport PR #6271 on branch v0.19.x (hough_line_peaks fix for corner case with optimal angle=0) (#6313)

  • Backport PR #6261 on branch v0.19.x (Ignore sparse matrix deprecation warning) (#6316)

  • backport PR 6328: Fix issue with newer versions of matplotlib in manual segmentation (#6334)

  • Backport PR #6343 on branch v0.19.x (avoid warnings about change to v3 API from imageio) (#6344)

  • Backport PR #6355 on branch v0.19.x (remove use of deprecated kwargs from test_tifffile_kwarg_passthrough) (#6357)

  • Backport PR #6352 on branch v0.19.x (Fix channel_axis default for cycle_spin) (#6358)

  • Backport PR #6348 on branch v0.19.x (Fix smoothed image computation when mask is None in canny) (#6359)

  • Backport PR #6361 on branch v0.19.x (Document support for Path objects in io functions) (#6363)

  • Backport PR #6400 on branch v0.19.x (Add support for NumPy 1.23) (#6403)

  • Backport PR #6335 on branch v0.19.x (warp/rotate: fixed a bug with clipping when cval is not in the input range) (#6411)

  • Backport PR #6413 on branch v0.19.x (Fix computation of histogram bins for multichannel integer-valued images) (#6414)

10 authors added to this release [alphabetical by first name or login]#

  • Albert Y. Shih

  • Bartłomiej Śmietanka

  • Dave Mellert

  • Gregory Lee

  • Graham Inggs

  • Jarrod Millman

  • John Hagen

  • Mark Harfouche

  • Riadh Fezzani

  • Stefan van der Walt

7 reviewers added to this release [alphabetical by first name or login]#

  • Alexandre de Siqueira

  • Gregory Lee

  • Jarrod Millman

  • Juan Nunez-Iglesias

  • Lars Grüter

  • Mark Harfouche

  • Riadh Fezzani

scikit-image 0.19.2 (2021-02-17)#

We’re happy to announce the release of scikit-image v0.19.2! This is primarily a bug fix release, although there is one new gallery example related to detection of fluorescence at the nuclear envelope of mammalian cells.

scikit-image is an image processing toolbox for SciPy that includes algorithms for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more.

For more information, examples, and documentation, please visit our website:

https://scikit-image.org

Pull Requests Included#

  • fix mistake in tests.yml made during backport (gh-6129)

  • Backport PR #6145 on branch v0.19.x (Fix channel_axis handling in pyramid_gaussian and pyramid_laplace) (gh-6155)

  • Backport PR #6130 on branch v0.19.x (bump deprecated Azure windows environment) (gh-6131)

  • Backport PR #6148 on branch v0.19.x (deprecate n_iter_max (should be max_num_iter)) (gh-6156)

  • Backport PR #6152 on branch v0.19.x (specify python version used by mybinder.org for gallery demos) (gh-6157)

  • Backport PR #6139 on branch v0.19.x (fix phase_cross_correlation typo) (gh-6158)

  • Backport PR #6133 on branch v0.19.x (Update user warning message for viewer module.) (gh-6159)

  • Backport PR #6169 on branch v0.19.x (Fix unintended change to output dtype of match_histograms) (gh-6172)

  • Backport PR #6184 on branch v0.19.x (Fix SIFT wrong octave indices + typo) (gh-6186)

  • Backport PR #6191 on branch v0.19.x (Fix issue6190 - inconsistent default parameters in pyramids.py) (gh-6193)

  • Backport PR #6207 on branch v0.19.x (Always set params to nan when ProjectiveTransform.estimate fails) (gh-6210)

  • Backport PR #5262 on branch v0.19.x (Add textbook-like tutorial on measuring fluorescence at nuclear envelope.) (gh-6213)

  • Backport PR #6087 on branch v0.19.x (Add two datasets for use in upcoming scientific tutorials.) (gh-6215)

  • Backport PR #6214 on branch v0.19.x (EuclideanTransform.estimate should return False when NaNs are present) (gh-6221)

  • Backport PR #6219 on branch v0.19.x (Allow the output_shape argument to be any iterable for resize and resize_local_mean) (gh-6222)

  • Backport PR #6223 on branch v0.19.x (Update filename in testing instructions.) (gh-6225)

  • Backport PR #6231 on branch v0.19.x (Update imports/refs from deprecated scipy.ndimage.filters namespace) (gh-6233)

  • Backport PR #6229 on branch v0.19.x (Remove redundant testing on Appveyor) (gh-6234)

  • Backport PR #6183 on branch v0.19.x (Fix decorators warnings stacklevel) (gh-6238)

  • Backport PR #6239 on branch v0.19.x (DOC: fix SciPy intersphinx) (gh-6241)

  • Backport PR #6232 on branch v0.19.x (Include Cython sources via package_data) (gh-6244)

  • Backport PR #6227 on branch v0.19.x (Fix calculation of Z normal in marching cubes) (gh-6245)

  • Backport PR #6242 on branch v0.19.x (Fix bug in SLIC superpixels with enforce_connectivity=True and start_label > 0) (gh-6246)

  • Backport PR #6211 on branch v0.19.x (PiecewiseAffineTransform.estimate return should reflect underlying transforms) gh-6247

  • update MacOS libomp installation in wheel building script (gh-6249)

9 authors added to this release [alphabetical by first name or login]#

  • Chris Roat

  • Fabian Schneider

  • Gregory Lee

  • Hande Gözükan

  • Larry Bradley

  • Marianne Corvellec

  • Mark Harfouche

  • Miles Lucas

  • Riadh Fezzani

8 reviewers added to this release [alphabetical by first name or login]#

  • Alexandre de Siqueira

  • Gregory Lee

  • Juan Nunez-Iglesias

  • Marianne Corvellec

  • Mark Harfouche

  • Riadh Fezzani

  • Robert Haase

  • Stefan van der Walt

scikit-image 0.19.1 (2021-12-03)#

We’re happy to announce the release of scikit-image v0.19.1!

This is a small bug fix release that resolves a couple of backwards compatibility issues and a couple of issues with the wheels on PyPI. Specifically, MacOs wheels for Apple M1 (arm64) on PyPI were broken in 0.19.0, but should now be repaired. The arm64 wheels are for MacOs >= 12 only. Wheel sizes are also greatly reduced relative to 0.19.0 by stripping debug symbols from the binaries and making sure that Cython-generated source files are not bundled in the wheels.

Pull Requests Included#

  • Backport PR #6089 on branch v0.19.x (Skip tests requiring fetched data) (gh-6115)

  • Backport PR #6097 on branch v0.19.x (restore non-underscore functions in skimage.data) (gh-6099)

  • Backport PR #6095 on branch v0.19.x (Preserve backwards compatibility for channel_axis parameter in transform functions) (gh-6100)

  • Backport PR #6103 on branch v0.19.x (make rank filter test comparisons robust across architectures) (gh-6106)

  • Backport PR #6105 on branch v0.19.x (pass a specific random_state into ransac in test_ransac_geometric) (gh-6107)

  • Fix two equality comparison bugs in the wheel build script (gh-6098)

  • Backport of gh-6109 (Add linker flags to strip debug symbols during wheel building) (gh-6110)

  • Pin setuptools maximum in v0.19.x to avoid breaking on planned distutils API changes (gh-6112)

  • Avoid potential circular import of rgb2gray (gh-6113)

  • Backport PR #6089 on branch v0.19.x (Skip tests requiring fetched data) (gh-6115)

  • Backport PR #6118 on branch v0.19.x (Fixes to tests.yml and fixes for expected warnings) (gh-6127)

  • Backport PR #6114 on branch v0.19.x (relax test condition to make it more robust to variable CI load) (gh-6128)

3 authors added to this release [alphabetical by first name or login]#

  • Gregory R. Lee

  • Joshua Newton

  • Mark Harfouche

5 reviewers added to this release [alphabetical by first name or login]#

  • Gregory R. Lee

  • Juan Nunez-Iglesias

  • Marianne Corvellec

  • Mark Harfouche

  • Stefan van der Walt

scikit-image 0.19.0 (2021-12-03)#

We’re happy to announce the release of scikit-image v0.19.0!

scikit-image is an image processing toolbox for SciPy that includes algorithms for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more.

For more information, examples, and documentation, please visit our website:

https://scikit-image.org

A highlight of this release is the addition of the popular scale-invariant feature transform (SIFT) feature detector and descriptor. This release also introduces a perceptual blur metric, new pixel graph algorithms, and most functions now operate in single-precision when single-precision inputs are provided. Many other bug fixes, enhancements and performance improvements are detailed below.

A significant change in this release is in the treatment of multichannel images. The existing multichannel argument to functions has been deprecated in favor of a new channel_axis argument. channel_axis can be used to specify which axis of an array contains channel information (with channel_axis=None indicating a grayscale image).

scikit-image now uses “lazy loading”, which enables users to access the functions from all skimage submodules without the overhead of eagerly importing all submodules. As a concrete example, after calling “import skimage” a user can directly call a function such as skimage.transform.warp whereas previously it would have been required to first “import skimage.transform”.

An exciting change on the development side is the introduction of support for Pythran as an alternative to Cython for generating compiled code. We plan to keep Cython support as well going forward, so developers are free to use either one as appropriate. For those curious about Pythran, a good overview was given in the SciPy 2021 presentation, “Building SciPy Kernels with Pythran” (https://www.youtube.com/watch?v=6a9D9WL6ZjQ).

This release now supports Python 3.7-3.10. Apple M1 architecture (arm64) support is new to this release. MacOS 12 wheels are provided for Python 3.8-3.10.

New Features#

  • Added support for processing images with channels located along any array axis. This is in contrast to previous releases where channels were required to be the last axis of an image. See more info on the new channel_axis argument under the API section of the release notes.

  • A no-reference measure of perceptual blur was added (skimage.measure.blur_effect).

  • Non-local means (skimage.restoration.denoise_nl_means) now supports 3D multichannel, 4D and 4D multichannel data when fast_mode=True.

  • An n-dimensional Fourier-domain Butterworth filter (skimage.filters.butterworth) was added.

  • Color conversion functions now have a new channel_axis keyword argument that allows specification of which axis of an array corresponds to channels. For backwards compatibility, this parameter defaults to channel_axis=-1, indicating that channels are along the last axis.

  • Added a new keyword only parameter random_state to morphology.medial_axis and restoration.unsupervised_wiener.

  • Seeding random number generators will not give the same results as the underlying generator was updated to use numpy.random.Generator.

  • Added saturation parameter to skimage.color.label2rgb

  • Added normalized mutual information metric skimage.metrics.normalized_mutual_information

  • threshold_local now supports n-dimensional inputs and anisotropic block_size

  • New skimage.util.label_points function for assigning labels to points.

  • Added nD support to several geometric transform classes

  • Added skimage.metrics.hausdorff_pair to find points separated by the Hausdorff distance.

  • Additional colorspace illuminants and observers parameter options were added to skimage.color.lab2rgb, skimage.color.rgb2lab, skimage.color.xyz2lab, skimage.color.lab2xyz, skimage.color.xyz2luv and skimage.color.luv2xyz.

  • skimage.filters.threshold_multiotsu has a new hist keyword argument to allow use with a user-supplied histogram. (gh-5543)

  • skimage.restoration.denoise_bilateral added support for images containing negative values. (gh-5527)

  • The skimage.feature functions blob_dog, blob_doh and blob_log now support a threshold_rel keyword argument that can be used to specify a relative threshold (in range [0, 1]) rather than an absolute one. (gh-5517)

  • Implement lazy submodule importing (gh-5101)

  • Implement weighted estimation of geometric transform matrices (gh-5601)

  • Added new pixel graph algorithms in skimage.graph: pixel_graph generates a graph (network) of pixels according to their adjacency, and central_pixel finds the geodesic center of the pixels. (gh-5602)

  • scikit-image now supports use of Pythran in contributed code. (gh-3226)

Documentation#

  • A new doc tutorial presenting a 3D biomedical imaging example has been added to the gallery (gh-4946). The technical content benefited from conversations with Genevieve Buckley, Kevin Mader, and Volker Hilsenstein.

  • New gallery example for 3D structure tensor.

  • New gallery example displaying a 3D dataset.

  • Extended rolling ball example with ECG data (1D).

  • The stain unmixing gallery example was fixed and now displays proper separation of the stains.

  • Documentation has been added to the contributing notes about how to submit a gallery example.

  • Autoformat docstrings in morphology.

  • Display plotly figures from gallery example even when running script at CLI.

  • Single out docs-only PRs in review process.

  • Use matplotlib’s infinite axline to demonstrate hough transform.

  • Clarify disk documentation inconsistency regarding ‘shape’.

  • docs: fix simple typo, conversions -> conversions.

  • Fixes to linspace in example.

  • Minor fixes to Hough line transform code and examples.

  • Added 1/2 pixel bounds to extent of displayed images in several examples.

  • Add release step on github to RELEASE.txt.

  • Remove reference to opencv in threshold_local documentation.

  • Update structure_tensor docstring to include per-axis sigma.

  • Fix typo in _shared/utils.py docs.

  • Proofread and crosslink examples with immunohistochemistry image.

  • Spelling correction: witch -> which.

  • Mention possible filters in radon_transform -> filtered-back-projection

  • Fix dtype info in documentation for watershed.

  • Proofread gallery example for Radon transform.

  • Use internal function for noise + clarify code in Canny example.

  • Make more comprehensive ‘see also’ sections in filters.

  • Specify the release note version instead of the misleading latest.

  • Remove misleading comment in plot_thresholding.py example.

  • Fix sphinx layout to make the search engine work with recent sphinx versions.

  • Draw node IDs in RAG example.

  • Update sigma_color description in denoise_bilateral.

  • Update intersphinx fallback inventories + add matplotlib fallback inventory.

  • Fix numpy deprecation in plot_local_equalize.py.

  • Rename label variable in plot_regionprops.py to circumvent link issue in docs.

  • Avoid duplicate API documentation for ImageViewer, CollectionViewer.

  • Fix ‘blog_dog’ typo in gaussian docs.

  • Update reference link documentation in the adjust_sigmoid function.

  • Fix reference to multiscale_basic_features in TrainableSegmenter.

  • Slight shape_index docstring modification to specify 2D array.

  • Add stitching gallery example (gh-5365)

  • Add draft SKIP3: transition to scikit-image 1.0 (gh-5475)

  • Mention commit messages in the contribution guidelines. (gh-5504)

  • Fix and standardize docstrings for blob detection functions. (gh-5547)

  • Update the User Guide to reflect usage of channel_axis rather than multichannel. (gh-5554)

  • Update the user guide to use channel_axis rather than multichannel (gh-5556)

  • Add hyperlinks to referenced documentation places. (gh-5560)

  • Update branching instructions to change the location of the pooch repo. (gh-5565)

  • Add Notes and References section to the Cascade class docstring. (gh-5568)

  • Clarify 2D vs nD in skimage.feature.corner docstrings (gh-5569)

  • Fix math formulas in plot_swirl.py example. (gh-5574)

  • Update references in texture feature detectors docstrings (gh-5578)

  • Update mailing list location to discuss.scientific-python.org forum (gh-5951)

  • DOC: Fix docstring in rescale_intensity() (gh-5964)

  • Fix slic documentation (gh-5975)

  • Update docstring for dilation, which is now nD. (gh-5978)

  • Change stitching gallery example thumbnail (gh-5985)

  • Add circle and disk to glossary.md (gh-5590)

  • Update pixel graphs example (gh-5991)

  • Separate entries that have the same description in glossary.md (gh-5592)

  • Do not use space before colon in directive name (gh-6002)

Improvements#

  • Many more functions throughout the library now have single precision (float32) support.

  • Biharmonic inpainting (skimage.restoration.inpaint_biharmonic) was refactored and is orders of magnitude faster than before.

  • Salt-and-pepper noise generation with skimage.util.random_noise is now faster.

  • The performance of the SLIC superpixels algorithm (skimage.segmentation.slice) was improved for the case where a mask is supplied by the user (gh-4903). The specific superpixels produced by masked SLIC will not be identical to those produced by prior releases.

  • exposure.adjust_gamma has been accelerated for uint8 images thanks to a LUT (gh-4966).

  • measure.label has been accelerated for boolean input images, by using scipy.ndimage’s implementation for this case (gh-4945).

  • util.apply_parallel now works with multichannel data (gh-4927).

  • skimage.feature.peak_local_max supports now any Minkowski distance.

  • Fast, non-Cython implementation for skimage.filters.correlate_sparse.

  • For efficiency, the histogram is now precomputed within skimage.filters.try_all_threshold.

  • Faster skimage.filters.find_local_max when given a finite num_peaks.

  • All filters in the skimage.filters.rank module now release the GIL, enabling multithreaded use.

  • skimage.restoration.denoise_tv_bregman and skimage.restoration.denoise_bilateral now release the GIL, enabling multithreaded use.

  • A skimage.color.label2rgb performance regression was addressed.

  • Improve numerical precision in CircleModel.estimate. (gh-5190)

  • Add default keyword argument values to skimage.restoration.denoise_tv_bregman, skimage.measure.block_reduce, and skimage.filters.threshold_local. (gh-5454)

  • Make matplotlib an optional dependency (gh-5990)

  • single precision support in skimage.filters (gh-5354)

  • Support nD images and labels in label2rgb (gh-5550)

  • Regionprops table performance refactor (gh-5576)

  • add regionprops benchmark script (gh-5579)

  • remove use of apply_along_axes from greycomatrix & greycoprops (gh-5580)

  • refactor gabor_kernel for efficiency (gh-5582)

  • remove need for channel_as_last_axis decorator in skimage.filters (gh-5584)

  • replace use of scipy.ndimage.gaussian_filter with skimage.filters.gaussian (gh-5872)

  • add channel_axis argument to quickshift (gh-5987)

  • add MacOS arm64 wheels (gh-6068)

API Changes#

  • The multichannel boolean argument has been deprecated. All functions with multichannel support now use an integer channel_axis to specify which axis corresponds to channels. Setting channel_axis to None is used to indicate that the image is grayscale. Specifically, existing code with multichannel=True should be updated to use channel_axis=-1 and code with multichannel=False should now specify channel_axis=None.

  • Most functions now return float32 images when the input has float32 dtype.

  • A default value has been added to measure.find_contours, corresponding to the half distance between the min and max values of the image (gh-4862).

  • data.cat has been introduced as an alias of data.chelsea for a more descriptive name.

  • The level parameter of measure.find_contours is now a keyword argument, with a default value set to (max(image) - min(image)) / 2.

  • p_norm argument was added to skimage.feature.peak_local_max to add support for Minkowski distances.

  • skimage.transforms.integral_image now promotes floating point inputs to double precision by default (for accuracy). A new dtype keyword argument can be used to override this behavior when desired.

  • Color conversion functions now have a new channel_axis keyword argument (see New Features section).

  • SLIC superpixel segmentation outputs may differ from previous versions for data that was not already scaled to [0, 1] range. There is now an automatic internal rescaling of the input to [0, 1] so that the compactness parameter has an effect that is independent of the input image’s scaling.

  • A bug fix to the phase normalization applied within skimage.register.phase_cross_correlation may result in a different result as compared to prior releases. The prior behavior of “unnormalized” cross correlation is still available by explicitly setting normalization=None. There is no change to the masked cross-correlation case, which uses a different algorithm.

Bugfixes#

  • Input labels argument renumbering in skimage.feature.peak_local_max is avoided (gh-5047).

  • fix clip bug in resize when anti_aliasing is applied (gh-5202)

  • Nonzero values at the image edge are no longer incorrectly marked as a boundary when using find_bounaries with mode=’subpixel’ (gh-5447).

  • Fix return dtype of _label2rgb_avg function.

  • Ensure skimage.color.separate_stains does not return negative values.

  • Prevent integer overflow in EllipseModel.

  • Fixed off-by one error in pixel bins in Hough line transform, skimage.transform.hough_line.

  • Handle 1D arrays properly in skimage.filters.gaussian.

  • Fix Laplacian matrix size bug in skimage.segmentation.random_walker.

  • Regionprops table (skimage.measure.regionprops_table) dtype bugfix.

  • Fix skimage.transform.rescale when using a small scale factor.

  • Fix skimage.measure.label segfault.

  • Watershed (skimage.segmentation.watershed): consider connectivity when calculating markers.

  • Fix skimage.transform.warp output dtype when order=0.

  • Fix multichannel intensity_image extra_properties in regionprops.

  • Fix error message for skimage.metric.structural_similarity when image is too small.

  • Do not mark image edges in ‘subpixel’ mode of skimage.segmentation.find_boundaries.

  • Fix behavior of skimage.exposure.is_low_contrast for boolean inputs.

  • Fix wrong syntax for the string argument of ValueError in skimage.metric.structural_similarity .

  • Fixed NaN issue in skimage.filters.threshold_otsu.

  • Fix skimage.feature.blob_dog docstring example and normalization.

  • Fix uint8 overflow in skimage.exposure.adjust_gamma.

  • Work with pooch 1.5.0 for fetching data (gh-5529).

  • The offsets attribute of skimage.graph.MCP is now public. (gh-5547)

  • Fix io.imread behavior with pathlib.Path inputs (gh-5543)

  • Make scikit-image imports from Pooch, compatible with pooch >= 1.5.0. (gh-5529)

  • Fix several broken doctests and restore doctesting on GitHub Actions. (gh-5505)

  • Fix broken doctests in skimage.exposure.histogram and skimage.measure.regionprops_table. (gh-5522)

  • Rescale image consistently during SLIC superpixel segmentation. (gh-5518)

  • Correct phase correlation in skimage.register.phase_cross_correlation. (gh-5461)

  • Fix hidden attribute ‘offsets’ in skimage.graph.MCP (gh-5551)

  • fix phase_cross_correlation for 3D with reference masks (gh-5559)

  • fix return shape of blob_log and blob_dog when no peaks are found (gh-5567)

  • Fix find contours key error (gh-5577)

  • Refactor measure.ransac and add warning when the estimated model is not valid (gh-5583)

  • Restore integer image rescaling for edge filters (gh-5589)

  • trainable_segmentation: re-raise in error case (gh-5600)

  • allow regionprops_table to be called with deprecated property names (gh-5908)

  • Fix weight calculation in fast mode of non-local means (gh-5923)

  • fix for #5948: lower boundary 1 for kernel_size in equalize_adapthist (gh-5949)

  • convert pathlib.Path to str in imsave (gh-5971)

  • Fix slic spacing (gh-5974)

  • Add small regularization to avoid zero-division in richardson_lucy (gh-5976)

  • Fix benchmark suite (watershed function was moved) (gh-5982)

  • catch QhullError and return empty array (convex_hull) (gh-6008)

  • add property getters for all newly deprecated regionprops names (gh-6000)

  • Fix the estimation of ellipsoid axis lengths in the 3D case (gh-6013)

  • Fix peak local max segfault (gh-6035)

  • Avoid circular import errors when EAGER_IMPORT=1 (gh-6042)

  • remove all use of the deprecated distutils package (gh-6044)

Deprecations#

Completed deprecations from prior releases#

  • In measure.label, the deprecated neighbors parameter has been removed (use connectivity instead).

  • The deprecated skimage.color.rgb2grey and skimage.color.grey2rgb functions have been removed (use skimage.color.rgb2gray and skimage.color.gray2rgb instead).

  • skimage.color.rgb2gray no longer allows grayscale or RGBA inputs.

  • The deprecated alpha parameter of skimage.color.gray2rgb has now been removed. Use skimage.color.gray2rgba for conversion to RGBA.

  • Attempting to warp a boolean image with order > 0 now raises a ValueError.

  • When warping or rescaling boolean images, setting anti-aliasing=True will raise a ValueError.

  • The bg_label parameter of skimage.color.label2rgb is now 0.

  • The deprecated filter parameter of skimage.transform.iradon has now been removed (use filter_name instead).

  • The deprecated skimage.draw.circle function has been removed (use skimage.draw.disk instead).

  • The deprecated skimage.feature.register_translation function has been removed (use skimage.registration.phase_cross_correlation instead).

  • The deprecated skimage.feature.masked_register_translation function has been removed (use skimage.registration.phase_cross_correlation instead).

  • The deprecated skimage.measure.marching_cubes_classic function has been removed (use skimage.measure.marching_cubes instead).

  • The deprecated skimage.measure.marching_cubes_lewiner function has been removed (use skimage.measure.marching_cubes instead).

  • The deprecated skimage.segmentation.circle_level_set function has been removed (use skimage.segmentation.disk_level_set instead).

  • The deprecated inplace parameter of skimage.morphology.flood_fill

  • The deprecated skimage.util.pad function has been removed (use numpy.pad instead). been removed (use in_place instead).

  • The default mode in skimage.filters.hessian is now 'reflect'.

  • The default boundary mode in skimage.filters.sato is now 'reflect'.

  • The default boundary mode in skimage.measure.profile_line is now 'reflect'.

  • The default value of preserve_range in skimage.restoration.denoise_nl_means is now False.

  • The default value of start_label in skimage.segmentation.slic is now 1.

Newly introduced deprecations:#

  • The multichannel argument is now deprecated throughout the library and will be removed in 1.0. The new channel_axis argument should be used instead. Existing code with multichannel=True should be updated to use channel_axis=-1 and code with multichannel=False should now specify channel_axis=None.

  • skimage.feature.greycomatrix and skimage.feature.greycoprops are deprecated in favor of skimage.feature.graycomatrix and skimage.feature.graycoprops.

  • The skimage.morphology.grey module has been renamed skimage.morphology.gray. The old name is deprecated.

  • The skimage.morphology.greyreconstruct module has been renamed skimage.morphology.grayreconstruct. The old name is deprecated.

  • see API Changes section regarding functions with deprecated argument names related to the number of iterations. num_iterations and max_num_iter are now used throughout the library.

  • see API Changes section on deprecation of the selem argument in favor of footprint throughout the library

  • Deprecate in_place in favor of the use of an explicit out argument in skimage.morphology.remove_small_objects, skimage.morphology.remove_small_holes and skimage.segmentation.clear_border

  • The input argument of skimage.measure.label has been renamed label_image. The old name is deprecated.

  • standardize on num_iter for parameters describing the number of iterations and max_num_iter for parameters specifying an iteration limit. Functions where the old argument names have now been deprecated are:

    skimage.filters.threshold_minimum
skimage.morphology.thin
skimage.restoration.denoise_tv_bregman
skimage.restoration.richardson_lucy
skimage.segmentation.active_contour
skimage.segmentation.chan_vese
skimage.segmentation.morphological_chan_vese
skimage.segmentation.morphological_geodesic_active_contour
skimage.segmentation.slic

  • The names of several parameters in skimage.measure.regionprops have been updated so that properties are better grouped by the first word(s) of the name. The old names will continue to work for backwards compatibility. The specific names that were updated are:

    ============================ ============================
Old Name                     New Name
============================ ============================
max_intensity                intensity_max
mean_intensity               intensity_mean
min_intensity                intensity_min

bbox_area                    area_bbox
convex_area                  area_convex
filled_area                  area_filled

convex_image                 image_convex
filled_image                 image_filled
intensity_image              image_intensity

local_centroid               centroid_local
weighted_centroid            centroid_weighted
weighted_local_centroid      centroid_weighted_local

major_axis_length            axis_major_length
minor_axis_length            axis_minor_length

weighted_moments             moments_weighted
weighted_moments_central     moments_weighted_central
weighted_moments_hu          moments_weighted_hu
weighted_moments_normalized  moments_weighted_normalized

equivalent_diameter          equivalent_diameter_area
============================ ============================

  • The selem argument has been renamed to footprint throughout the library. The selem argument is now deprecated.

Development process#

  • Test setup and teardown functions added to allow raising an error on any uncaught warnings via SKIMAGE_TEST_STRICT_WARNINGS_GLOBAL environment variable.

  • Increase automation in release process.

  • Release wheels before source

  • update minimum supported Matplotlib, NumPy, SciPy and Pillow

  • Pin pillow to !=8.3.0

  • Rename master to main throughout

  • Ensure that README.txt has write permissions for subsequent imports.

  • Run face classification gallery example with a single thread

  • Enable pip and skimage.data caching on Azure

  • Fix CircleCI and Azure CI caching.

  • Address Cython warnings.

  • Disable calls to plotly.io.show when running on Azure.

  • Remove legacy Travis-CI scripts and update contributor documentation accordingly.

  • Increase cibuildwheel verbosity.

  • Update pip during dev environment installation.

  • Add benchmark checks to CI.

  • Resolve stochastic rank filter test failures on CI.

  • Ensure that README.txt has write permissions for subsequent imports.

  • Decorators for helping with the transition between the keyword argument multichannel and channel_axis.

  • Add missing import in lch2lab docstring example (gh-5998)

  • Prefer importing build_py and sdist from setuptools (gh-6007)

  • Reintroduce skimage.test utility (gh-5909)

Other Updates#

  • Refactor np.random.x to use np.random.Generator.

  • Avoid warnings about use of deprecated scipy.linalg.pinv2.

  • Simplify resize implementation using new SciPy 1.6 zoom option.

  • Fix duplicate test function names in test_unsharp_mask.py.

  • Benchmarks: fix ResizeLocalMeanSuite.time_resize_local_mean signature.

  • Prefer use of new-style NumPy random API in tests (gh-5450)

  • Add fixture enforcing SimpleITK I/O in test_simpleitk.py (gh-5526)

  • MNT: Remove unused stat import from skimage data (gh-5566)

  • MAINT: Remove unused imports (gh-5595)

  • MAINT: Refactor duplicated tests, remove unnecessary assignments and variables (gh-5596)

  • Remove obsolete lazy import (gh-5992)

  • Lazily load data_dir into the top-level namespace (gh-5996)

  • Update scipy requirement to 1.4.1 and use scipy.fft instead of scipy.fftpack (gh-5999)

  • Remove lines generating Requires metadata (gh-6017)

  • Update wheel builds to include Python 3.10 (gh-6021)

  • Update pyproject.toml to handle Python 3.10 and Apple arm64 (gh-6022)

  • Add python 3.10 test runs on GitHub Actions and Appveyor (gh-6027)

  • Pin sphinx to <4.3 until new sphinx-gallery release is available (gh-6029)

  • Relax a couple of equality tests causing i686 test failures on cibuildwheel (gh-6031)

  • Avoid matplotlib import overhead during ‘import skimage’ (gh-6032)

  • Update sphinx gallery pin (gh-6034)

Contributors to this release#

80 authors added to this release [alphabetical by first name or login]#

  • Abhinavmishra8960 (Abhinavmishra8960)

  • abouysso

  • Alessia Marcolini

  • Alex Brooks

  • Alexandre de Siqueira

  • Andres Fernandez

  • Andrew Hurlbatt

  • andrewnags (andrewnags)

  • Antoine Bierret

  • BMaster123 (BMaster123)

  • Boaz Mohar

  • Bozhidar Karaargirov

  • Carlos Andrés Álvarez Restrepo

  • Christoph Gohlke

  • Christoph Sommer

  • Clement Ng

  • cmarasinou

  • Cris Luengo

  • David Manthey

  • Devanshu Shah

  • Dhiraj Kumar Sah

  • divyank agarwal

  • Egor Panfilov

  • Emmanuelle Gouillart

  • Erik Reed

  • erykoff (erykoff)

  • Fabian Schneider

  • Felipe Gutierrez-Barragan

  • François Boulogne

  • Fred Bunt

  • Fukai Yohsuke

  • Gregory R. Lee

  • Hari Prasad

  • Harish Venkataraman

  • Harshit Dixit

  • Ian Hunt-Isaak

  • Jaime Rodríguez-Guerra

  • Jan-Hendrik Müller

  • Janakarajan Natarajan

  • Jenny Vo

  • john lee

  • Jonathan Striebel

  • Joseph Fox-Rabinovitz

  • Juan Antonio Barragan Noguera

  • Juan Nunez-Iglesias

  • Julien Jerphanion

  • Jurneo

  • klaussfreire (klaussfreire)

  • Larkinnjm1 (Larkinnjm1)

  • Lars Grüter

  • Mads Dyrmann

  • Marianne Corvellec

  • Marios Achilias

  • Mark Boer

  • Mark Harfouche

  • Matthias Bussonnier

  • Mauro Silberberg

  • Max Frei

  • michalkrawczyk (michalkrawczyk)

  • Niels Cautaerts

  • Pamphile ROY

  • Pradyumna Rahul

  • R

  • Raphael

  • Riadh Fezzani

  • Robert Haase

  • Sebastian Gonzalez Tirado

  • Sebastián Vanrell

  • serge-sans-paille (serge-sans-paille)

  • Stefan van der Walt

  • t.ae

  • that1solodev (Xyno18)

  • Thomas Walter

  • Tim Gates

  • Tom Flux

  • Vinicius D. Cerutti

  • Volker Hilsenstein

  • WeiChungChang

  • yacth

  • Yash-10 (Yash-10)

63 reviewers added to this release [alphabetical by first name or login]#

  • Abhinavmishra8960

  • Alessia Marcolini

  • Alex Brooks

  • Alexandre de Siqueira

  • Andres Fernandez

  • Andrew Hurlbatt

  • andrewnags

  • BMaster123

  • Boaz Mohar

  • Carlos Andrés Álvarez Restrepo

  • Clement Ng

  • Cris Luengo

  • Dan Schult

  • David Manthey

  • Egor Panfilov

  • Emmanuelle Gouillart

  • erykoff

  • Fabian Schneider

  • Felipe Gutierrez-Barragan

  • François Boulogne

  • Fukai Yohsuke

  • Genevieve Buckley

  • Gregory R. Lee

  • Jan Eglinger

  • Jan-Hendrik Müller

  • Janakarajan Natarajan

  • Jarrod Millman

  • Jirka Borovec

  • Joan Massich

  • Johannes Schönberger

  • john lee

  • Jon Crall

  • Joseph Fox-Rabinovitz

  • Josh Warner

  • Juan Nunez-Iglesias

  • Julien Jerphanion

  • Kenneth Hoste

  • klaussfreire

  • Larkinnjm1

  • Lars Grüter

  • Marianne Corvellec

  • Mark Boer

  • Mark Harfouche

  • Matthias Bussonnier

  • Max Frei

  • michalkrawczyk

  • Niels Cautaerts

  • Pamphile ROY

  • Pomax

  • R

  • Raphael

  • Riadh Fezzani

  • Robert Kern

  • Ross Barnowski

  • Sebastian Berg

  • Sebastian Gonzalez Tirado

  • Sebastian Wallkötter

  • serge-sans-paille

  • Stefan van der Walt

  • t.ae

  • Vinicius D. Cerutti

  • Volker Hilsenstein

  • Yash-10