scikit-image 0.20.0 (2023-02-28)#

scikit-image is an image processing toolbox built on 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

With this release, many of the functions in skimage.measure now support anisotropic images with different voxel spacings.

Many performance improvements were made, such as support for footprint decomposition in skimage.morphology

Four new gallery examples were added to the documentation, including the new interactive example “Track solidification of a metallic alloy”.

This release completes the transition to a more flexible channel_axis parameter for indicating multi-channel images, and includes several other deprecations that make the API more consistent and expressive.

Finally, in preparation for the removal of distutils in the upcoming Python 3.12 release, we replaced our build system with meson and a static pyproject.toml specification.

This release supports Python 3.8–3.11.

New features and improvements#

  • Support footprint decomposition to several footprint generating and consuming functions in skimage.morphology. By decomposing a footprint into several smaller ones, morphological operations can potentially be sped up. The decomposed footprint can be generated with the new decomposition parameter of the functions rectangle, diamond, disk, cube, octahedron, ball, and octagon in skimage.morphology. The footprint parameter of the functions binary_erosion, binary_dilation, binary_opening, binary_closing, erosion, dilation, opening, closing, white_tophat, and black_tophat in skimage.morphology now accepts a sequence of 2-element tuples (footprint_i, num_iter_i) where each entry, i, of the sequence contains a footprint and the number of times it should be iteratively applied. This is the form produced by the footprint decompositions mentioned above (#5482, #6151).

  • Support anisotropic images with different voxel spacings. Spacings can be defined with the new parameter spacing of the following functions in skimage.measure: regionprops, regionprops_table, moments, moments_central, moments_normalized, centroid, inertia_tensor, and inertia_tensor_eigvals. Voxel spacing is taken into account for the following existing properties in skimage.measure.regionprops: area, area_bbox, centroid, area_convex, extent, feret_diameter_max, area_filled, inertia_tensor, moments, moments_central, moments_hu, moments_normalized, perimeter, perimeter_crofton, solidity, moments_weighted_central, and moments_weighted_hu. The new properties num_pixels and coords_scaled are available as well. See the respective docstrings for more details (#6296).

  • Add isotropic binary morphological operators isotropic_closing, isotropic_dilation, isotropic_erosion, and isotropic_opening in skimage.morphology. These functions return the same results as their non-isotropic counterparts but perform faster for large circular structuring elements (#6492).

  • Add new colocalization metrics pearson_corr_coeff, manders_coloc_coeff, manders_overlap_coeff and intersection_coeff to skimage.measure (#6189).

  • Support the Modified Hausdorff Distance (MHD) metric in skimage.metrics.hausdorff_distance via the new parameter method. The MHD can be more robust against outliers than the directed Hausdorff Distance (HD) (#5581).

  • Add two datasets skimage.data.protein_transport and skimage.data.nickel_solidification (#6087).

  • Add new parameter use_gaussian_derivatives to skimage.feature.hessian_matrix which allows the computation of the Hessian matrix by convolving with Gaussian derivatives (#6149).

  • Add new parameters squared_butterworth and npad to skimage.filters.butterworth, which support traditional or squared filtering and edge padding, respectively (#6251).

  • Support construction of a skimage.io.ImageCollection from a load_pattern with an arbitrary sequence as long as a matching load_func is provided (#6276).

  • Add new parameter alpha to skimage.metrics.adapted_rand_error allowing control over the weight given to precision and recall (#6472).

  • Add new parameter binarize to skimage.measure.grid_points_in_poly to optionally return labels that tell whether a pixel is inside, outside, or on the border of the polygon (#6515).

  • Add new parameter include_borders to skimage.measure.convex_hull_image to optionally exclude vertices or edges from the final hull mask (#6515).

  • Add new parameter offsets to skimage.measure.regionprops that optionally allows specifying the coordinates of the origin and affects the properties coords_scaled and coords (#3706).

  • Add new parameter disambiguate to skimage.registration.phase_cross_correlation to optionally disambiguate periodic shifts (#6617).

  • Support n-dimensional images in skimage.filters.farid (Farid & Simoncelli filter) (#6257).

  • Support n-dimensional images in skimage.restoration.wiener (#6454).

  • Support three dimensions for the properties rotation and translation in skimage.transform.EuclideanTransform as well as for skimage.transform.SimilarityTransform.scale (#6367).

  • Allow footprints with non-adjacent pixels as neighbors in skimage.morphology.flood_fill (#6236).

  • Support array-likes consistently in AffineTransform, EssentialMatrixTransform, EuclideanTransform, FundamentalMatrixTransform, GeometricTransform, PiecewiseAffineTransform, PolynomialTransform, ProjectiveTransform, SimilarityTransform, estimate_transform, and matrix_transform in skimage.transform (#6270).

Performance#

  • Improve performance (~2x speedup) of skimage.feature.canny by porting a part of its implementation to Cython (#6387).

  • Improve performance (~2x speedup) of skimage.feature.hessian_matrix_eigvals and 2D skimage.feature.structure_tensor_eigenvalues (#6441).

  • Improve performance of skimage.measure.moments_central by avoiding redundant computations (#6188).

  • Reduce import time of skimage.io by loading the matplotlib plugin only when required (#6550).

  • Incorporate RANSAC improvements from scikit-learn into skimage.measure.ransac which decrease the number of iterations (#6046).

  • Improve histogram matching performance on unsigned integer data with skimage.exposure.match_histograms. (#6209, #6354).

  • Reduce memory consumption of the ridge filters meijering, sato, frangi, and hessian in skimage.filters (#6509).

  • Reduce memory consumption of blob_dog, blob_log, and blob_doh in skimage.feature (#6597).

  • Use minimal required unsigned integer size internally in skimage.morphology.reconstruction which allows to operate the function with higher precision or on larger arrays. Previously, int32 was used. (#6342).

  • Use minimal required unsigned integer size in skimage.filters.rank_order which allows to operate the function with higher precision or on larger arrays. Previously, the returned labels and original_values were always of type uint32. (#6342).

Changes and new deprecations#

  • Set Python 3.8 as the minimal supported version (#6679).

  • Rewrite skimage.filters.meijering, skimage.filters.sato, skimage.filters.frangi, and skimage.filters.hessian to match the published algorithms more closely. This change is backward incompatible and will lead to different output values compared to the previous implementation. The Hessian matrix calculation is now done more accurately. The filters will now be correctly set to zero whenever one of the Hessian eigenvalues has a sign which is incompatible with a ridge of the desired polarity. The gamma constant of the Frangi filter is now set adaptively based on the maximum Hessian norm (#6446).

  • Move functions in skimage.future.graph to skimage.graph. This affects cut_threshold, cut_normalized, merge_hierarchical, rag_mean_color, RAG, show_rag, and rag_boundary (#6674).

  • Return False in skimage.measure.LineModelND.estimate instead of raising an error if the model is under-determined (#6453).

  • Return False in skimage.measure.CircleModel.estimate instead of warning if the model is under-determined (#6453).

  • Rename skimage.filters.inverse to skimage.filters.inverse_filter. skimage.filters.inverse is deprecated and will be removed in the next release (#6418, #6701).

  • Update minimal supported dependencies to numpy>=1.20 (#6565).

  • Update minimal supported dependencies to scipy>=1.8 (#6564).

  • Update minimal supported dependencies to networkx>=2.8 (#6564).

  • Update minimal supported dependency to pillow>=9.0.1 (#6402).

  • Update minimal supported dependency to setuptools 67 (#6754).

  • Update optional, minimal supported dependency to matplotlib>=3.3 (#6383).

  • Warn for non-integer image inputs to skimage.feature.local_binary_pattern. Applying the function to floating-point images may give unexpected results when small numerical differences between adjacent pixels are present (#6272).

  • Warn if skimage.registration.phase_cross_correlation returns only the shift vector. Starting with the next release this function will always return a tuple of three (shift vector, error, phase difference). Use return_error="always" to silence this warning and switch to this new behavior (#6543).

  • Warn in skimage.metrics.structural_similarity, if data_range is not specified in case of floating point data (#6612).

  • Automatic detection of the color channel is deprecated in skimage.filters.gaussian and a warning is emitted if the parameter channel_axis is not set explicitly (#6583).

Completed deprecations#

  • Remove skimage.viewer which was scheduled for removal in the postponed version 1.0 (#6160).

  • Remove deprecated parameter indices from skimage.feature.peak_local_max (#6161).

  • Remove skimage.feature.structure_tensor_eigvals (it was replaced by skimage.feature.structure_tensor_eigenvalues) and change the default parameter value in skimage.feature.structure_tensor to order="rc" (#6162).

  • Remove deprecated parameter array in favor of image from skimage.measure.find_contours (#6163).

  • Remove deprecated Qt IO plugin and the skivi console script (#6164).

  • Remove deprecated parameter value method='_lorensen' in skimage.measure.marching_cubes (#6230).

  • Remove deprecated parameter multichannel; use channel_axis instead. This affects skimage.draw.random_shapes, skimage.exposure.match_histograms, skimage.feature.multiscale_basic_features, skimage.feature.hog, skimage.feature.difference_of_gaussians, skimage.filters.unsharp_mask, and skimage.metrics.structural_similarity. In skimage.restoration, this affects cycle_spin, denoise_bilateral, denoise_tv_bregman, denoise_tv_chambolle, denoise_wavelet, estimate_sigma, inpaint_biharmonic, and denoise_nl_means. In skimage.segmentation, this affects felzenszwalb, random_walker, and slic. In skimage.transform, this affects rescale, warp_polar, pyramid_reduce, pyramid_expand, pyramid_gaussian, and pyramid_laplacian. In skimage.util, this affects montage and apply_parallel (#6583).

  • Remove deprecated parameter selem; use footprint instead. In skimage.filters, this affects median, autolevel_percentile, gradient_percentile, mean_percentile, subtract_mean_percentile, enhance_contrast_percentile, percentile, pop_percentile, sum_percentile, threshold_percentile, mean_bilateral, pop_bilateral, sum_bilateral, autolevel, equalize, gradient, maximum, mean, geometric_mean, subtract_mean, median, minimum, modal, enhance_contrast, pop, sum, threshold, noise_filter, entropy, otsu, windowed_histogram, and majority. In skimage.morphology, this affects flood_fill, flood, binary_erosion, binary_dilation, binary_opening, binary_closing, h_maxima, h_minima, local_maxima, local_minima, erosion, dilation, opening, closing, white_tophat, black_tophat, and reconstruction (#6583).

  • Remove deprecated parameter max_iter from skimage.filters.threshold_minimum, skimage.morphology.thin, and skimage.segmentation.chan_vese; use max_num_iter instead (#6583).

  • Remove deprecated parameter max_iterations from skimage.segmentation.active_contour; use max_num_iter instead (#6583).

  • Remove deprecated parameter input from skimage.measure.label; use label_image instead (#6583).

  • Remove deprecated parameter coordinates from skimage.measure.regionprops and skimage.segmentation.active_contour (#6583).

  • Remove deprecated parameter neighbourhood from skimage.measure.perimeter; use neighborhood instead (#6583).

  • Remove deprecated parameters height and width from skimage.morphology.rectangle; use ncols and nrows instead (#6583).

  • Remove deprecated parameter in_place from skimage.morphology.remove_small_objects, skimage.morphology.remove_small_holes, and skimage.segmentation.clear_border; use out instead (#6583).

  • Remove deprecated parameter iterations from skimage.restoration.richardson_lucy, skimage.segmentation.morphological_chan_vese, and skimage.segmentation.morphological_geodesic_active_contour; use num_iter instead (#6583).

  • Remove support for deprecated keys "min_iter" and "max_iter" in skimage.restoration.unsupervised_wiener’s parameter user_params; use "min_num_iter" and "max_num_iter" instead (#6583).

  • Remove deprecated functions greycomatrix and greycoprops from skimage.feature (#6583).

  • Remove deprecated submodules skimage.morphology.grey and skimage.morphology.greyreconstruct; use skimage.morphology instead (#6583).

  • Remove deprecated submodule skimage.morphology.selem; use skimage.morphology.footprints instead (#6583).

  • Remove deprecated skimage.future.graph.ncut (it was replaced by skimage.graph.cut_normalized) (#6685).

Bug fixes#

  • Fix round-off error in skimage.exposure.adjust_gamma (#6285).

  • Round and convert output coordinates of skimage.draw.rectangle to int even if the input coordinates use float. This fix ensures that the output can be used for indexing similar to other draw functions (#6501).

  • Avoid unexpected exclusion of peaks near the image border in skimage.feature.peak_local_max if the peak value is smaller 0 (#6502).

  • Avoid anti-aliasing in skimage.transform.resize by default when using nearest neighbor interpolation (order == 0) with an integer input data type (#6503).

  • Use mask during rescaling in skimage.segmentation.slic. Previously, the mask was ignored when rescaling the image to make choice of compactness insensitive to the image values. The new behavior makes it possible to mask values such as numpy.nan or numpy.infinity. Additionally, raise an error if the input image has two dimensions and a channel_axis is specified - indicating that the image is multi-channel (#6525).

  • Fix unexpected error when passing a tuple to the parameter exclude_border in skimage.feature.blog_dog and skimage.feature.blob_log (#6533).

  • Raise a specific error message in skimage.segmentation.random_walker if no seeds are provided as positive values in the parameter labels (#6562).

  • Raise a specific error message when accessing region properties from skimage.measure.regionprops when the required intensity_image is unavailable (#6584).

  • Avoid errors in skimage.feature.ORB.detect_and_extract by breaking early if the octave image is too small (#6590).

  • Fix skimage.restoration.inpaint_biharmonic for images with Fortran-ordered memory layout (#6263).

  • Fix automatic detection of the color channel in skimage.filters.gaussian (this behavior is deprecated, see new deprecations) (#6583).

  • Fix stacklevel of warning in skimage.color.lab2rgb (#6616).

  • Fix the order of return values for skimage.feature.hessian_matrix and raise an error if order='xy' is requested for images with more than 2 dimensions (#6624).

  • Fix misleading exception in functions in skimage.filters.rank that did not mention that 2D images are also supported (#6666).

  • Fix in-place merging of wheights in skimage.graph.RAG.merge_nodes (#6692).

  • Fix growing memory error and silence compiler warning in internal heappush function (#6727).

  • Fix compiliation warning about struct initialization in Cascade.detect_multi_scale (#6728).

Documentation#

New#

  • Add gallery example “Decompose flat footprints (structuring elements)” (#6151).

  • Add gallery example “Butterworth Filters” and improve docstring of skimage.filters.butterworth (#6251).

  • Add gallery example “Render text onto an image” (#6431).

  • Add gallery example “Track solidification of a metallic alloy” (#6469).

  • Add gallery example “Colocalization metrics” (#6189).

  • Add support page (.github/SUPPORT.md) to help users from GitHub find appropriate support resources (#6171, #6575).

  • Add CITATION.bib to repository to help with citing scikit-image (#6195).

  • Add usage instructions for new Meson-based build system with dev.py (#6600).

Improved & updated#

  • Improve gallery example “Measure perimeters with different estimators” (#6200, #6121).

  • Adapt gallery example “Build image pyramids” to more diversified shaped images and downsample factors (#6293).

  • Adapt gallery example “Explore 3D images (of cells)” with interactive slice explorer using plotly (#4953).

  • Clarify meaning of the weights term and rewrite docstrings of skimage.restoration.denoise_tv_bregman and skimage.restoration.denoise_tv_chambolle (#6544).

  • Describe the behavior of skimage.io.MultiImage more precisely in its docstring (#6290, #6292).

  • Clarify that the enabled watershed_line parameter will not catch borders between adjacent marker regions in skimage.segmentation.watershed (#6280).

  • Clarify that skimage.morphology.skeletonize accepts an image of any input type (#6322).

  • Use gridded thumbnails in our gallery to demonstrate the different images and datasets available in skimage.data (#6298, #6300, #6301).

  • Tweak balance in the docstring example of skimage.restoration.wiener for a less blurry result (#6265).

  • Document support for Path objects in skimage.io.imread and skimage.io.imsave (#6361).

  • Improve error message in skimage.filters.threshold_multiotsu if the discretized image cannot be thresholded (#6375).

  • Show original unlabeled image as well in the gallery example “Expand segmentation labels without overlap” (#6396).

  • Document refactoring of grey* to skimage.feature.graymatrix and skimage.feature.graycoprops in the release 0.19 (#6420).

  • Document inclusion criteria for new functionality in core developer guide (#6488).

  • Print the number of segments after applying the Watershed in the gallery example “Comparison of segmentation and superpixel algorithms” (#6535).

  • Replace issue templates with issue forms (#6554, #6576).

  • Expand reviewer guidelines in pull request template (#6208).

  • Provide pre-commit PR instructions in pull request template (#6578).

  • Warn about and explain the handling of floating-point data in the docstring of skimage.metricts.structural_similarity (#6595).

  • Fix intensity autoscaling in animated imshow in gallery example “Measure fluorescence intensity at the nuclear envelope” (#6599).

  • Clarify dependency on scikit-image[data] and pooch in INSTALL.rst (#6619).

  • Don’t use confusing loop in installation instructions for conda (#6672).

  • Document value ranges of L*a*b* and L*Ch in lab2xyz, rgb2lab, lab2lch, and lch2lab in skimage.color (#6688, #6697, #6719).

  • Use more consistent style in docstring of skimage.feature.local_binary_pattern (#6736).

Fixes, spelling & minor tweaks#

  • Remove deprecated reference and use skimage.measure.marching_cubes in gallery example “Marching Cubes” (#6377).

  • List only the two primary OS-independent methods of installing scikit-image (#6557, #6560).

  • Fix description of connectivity parameter in the docstring of skimage.morphology.flood (#6534).

  • Fix formatting in the docstring of skimage.metrics.hausdorff_distance (#6203).

  • Fix typo in docstring of skimage.measure.moments_hu (#6016).

  • Fix formatting of mode parameter in skimage.util.random_noise (#6532).

  • Fix broken links in SKIP 3 (#6445).

  • Fix broken link in docstring of skimage.filters.sobel (#6474).

  • Change “neighbour” to EN-US spelling “neighbor” (#6204).

  • Add missing copyrights to LICENSE.txt and use formatting according to SPDX identifiers (#6419).

  • Include skimage.morphology.footprint_from_sequence in the public API documentation (#6555).

  • Correct note about return type in the docstring of skimage.exposure.rescale_intensity (#6582).

  • Stop using the git:// connection protocol and remove references to it (#6201, #6283).

  • Update scikit-image’s mailing addresses to the new domain discuss.scientific-python.org (#6255).

  • Remove references to deprecated mailing list in doc/source/user_guide/getting_help.rst (#6575).

  • Use “center” in favor of “centre”, and “color” in favor of “colour” gallery examples (#6421, #6422).

  • Replace reference to api_changes.rst with release_dev.rst (#6495).

  • Clarify header pointing to notes for latest version released (#6508).

  • Add missing spaces to error message in skimage.measure.regionprops (#6545).

  • Apply codespell to fix common spelling mistakes (#6537).

  • Add missing space in math directive in normalized_mutual_information’s docstring (#6549).

  • Fix lengths of docstring heading underline in skimage.morphology.isotropic_ functions (#6628).

  • Fix plot order due to duplicate examples with the file name plot_thresholding.py (#6644).

  • Get rid of numpy deprecation warning in gallery example plot_equalize (#6650).

  • Fix swapping of opening and closing in gallery example plot_rank_filters (#6652).

  • Get rid of numpy deprecation warning in gallery example in plot_log_gamma.py (#6655).

  • Remove warnings and unnecessary messages in gallery example “Tinting gray-scale images” (#6656).

  • Update the contribution guide to recommend creating the virtualenv outside the source tree (#6675).

  • Fix typo in docstring of skimage.data.coffee (#6740).

  • Add missing backtick in docstring of skimage.graph.merge_nodes (#6741).

  • Fix typo in skimage.metrics.variation_of_information (#6768).

71 authors contributed to this release [alphabetical by first name or login]#

  • Adeel Hassan

  • Albert Y. Shih

  • AleixBP (AleixBP)

  • Alex (sashashura)

  • Alexandr Kalinin

  • Alexandre de Siqueira

  • Amin (MOAMSA)

  • Antony Lee

  • Balint Varga

  • Ben Greiner

  • bsmietanka (bsmietanka)

  • Chris Roat

  • Chris Wood

  • Daria

  • Dave Mellert

  • Dudu Lasry

  • Elena Pascal

  • Eli Schwartz

  • Fabian Schneider

  • forgeRW (forgeRW)

  • Frank A. Krueger

  • Gregory Lee

  • Gus Becker

  • Hande Gözükan

  • Jacob Rosenthal

  • James Gao

  • Jan Kadlec

  • Jan-Hendrik Müller

  • Jan-Lukas Wynen

  • Jarrod Millman

  • Jeremy Muhlich

  • johnthagen (johnthagen)

  • Joshua Newton

  • Juan DF

  • Juan Nunez-Iglesias

  • Judd Storrs

  • Larry Bradley

  • Lars Grüter

  • lihaitao (li1127217ye)

  • Lucas Johnson

  • Malinda (maldil)

  • Marianne Corvellec

  • Mark Harfouche

  • Martijn Courteaux

  • Marvin Albert

  • Matthew Brett

  • Matthias Bussonnier

  • Miles Lucas

  • Nathan Chan

  • Naveen

  • OBgoneSouth (OBgoneSouth)

  • Oren Amsalem

  • Preston Buscay

  • Peter Sobolewski

  • Peter Bell

  • Ray Bell

  • Riadh Fezzani

  • Robin Thibaut

  • Ross Barnowski

  • samtygier (samtygier)

  • Sandeep N Menon

  • Sanghyeok Hyun

  • Sebastian Berg

  • Sebastian Wallkötter

  • Simon-Martin Schröder

  • Stefan van der Walt

  • Teemu Kumpumäki

  • Thanushi Peiris

  • Thomas Voigtmann

  • Tim-Oliver Buchholz

  • Tyler Reddy

42 reviewers contributed to this release [alphabetical by first name or login]#

  • Abhijeet Parida

  • Albert Y. Shih

  • Alex (sashashura)

  • Alexandre de Siqueira

  • Antony Lee

  • Ben Greiner

  • Carlo Dri

  • Chris Roat

  • Daniele Nicolodi

  • Daria

  • Dudu Lasry

  • Eli Schwartz

  • François Boulogne

  • Gregory Lee

  • Gus Becker

  • Jacob Rosenthal

  • James Gao

  • Jan-Hendrik Müller

  • Jarrod Millman

  • Juan DF

  • Juan Nunez-Iglesias

  • Lars Grüter

  • Malinda (maldil)

  • Marianne Corvellec

  • Mark Harfouche

  • Martijn Courteaux

  • Marvin Albert

  • Matthias Bussonnier

  • Oren Amsalem

  • Ralf Gommers

  • Riadh Fezzani

  • Robert Haase

  • Robin Thibaut

  • Sandeep N Menon

  • Sanghyeok Hyun

  • Sebastian Berg

  • Sebastian Wallkötter

  • Simon-Martin Schröder

  • Stefan van der Walt

  • Thanushi Peiris

  • Thomas Voigtmann

  • Tim-Oliver Buchholz

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