Announcement: scikit-image 0.18.0

We're happy to announce the release of scikit-image v0.18.0!

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.

This release of scikit-image drops support for Python 3.6 in accordance with
the NEP-29 Python and Numpy version support community standard <https://numpy.org/neps/nep-0029-deprecation_policy.html>_: Python 3.7 or
newer is required to run this version.

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

https://scikit-image.org

New Features

• Add the iterative Lucas-Kanade (iLK) optical flow method (#4161)
• Add Feret diameter in region properties (#4379, #4820)
• Add functions to compute Euler number and Crofton perimeter estimation (#4380)
• Add a function to compute the Hausdorff distance (#4382)
• Added 3D support for many filters in skimage.filters.rank.
• An experimental implementation of trainable pixel segmentation, aiming for
  compatibility with the scikit-learn API, has been added to
  skimage.future. Try it out! (#4739)
• Add a new function segmentation.expand_labels to dilate labels while
  preventing overlap (#4795)
• It is now possible to pass extra measurement functions to
  measure.regionprops and regionprops_table (#4810)
• Add rolling ball algorithm for background subtraction (#4851)
• New sample images have been added in the data subpackage: data.eagle
  (#4922), data.human_mitosis (#4939), data.cells3d (#4951), and
  data.vortex (#5041). Also note that the image for data.camera has
  been changed due to copyright issues (#4913).
• skimage.feature.structure_tensor now supports 3D (and nD) images as input
  (#5002)
• Many thresholding methods can now receive a precomputed histogram as input,
  resulting in significant speedups if multiple methods are tried on the same
  image, or if a fast histogram method is used. (#5006)
• measure.regionprops now supports multichannel intensity images (#5037)

Documentation

• Add an example to the flood fill tutorial (#4619)
• Docstring enhancements for marching cubes and find_contours (#4641)
• A new tutorial presenting a cell biology example has been added to the
  gallery (#4648). Special thanks to Pierre Poulain and Fred Bernard
  (Université de Paris and Institut Jacques Monod) for scientific review of
  this example!
• Improve register rotation example with notes and references (#4723)
• Add versionadded for new scalar type support for "scale" param in
  transform.AffineTransform (#4733)
• New tutorial on visualizing 3D data <https://scikit-image.org/docs/dev/auto_examples/applications/plot_3d_image_processing.html>_ (#4850)
• Add example for 3D adaptive histogram equalization (AHE) (#4658)
• Automatic formatting of docstrings for improved consistency (#4849)
• Improved docstring for rgb2lab (#4839) and marching_cubes (#4846)
• Improved docstring for measure.marching_cubes, mentioning how to decimate a
  mesh using mayavi (#4846)
• Document how to contribute a gallery example. (#4857)
• Fix and improve entropy example (#4904)
• expand the benchmarking section of the developer docs (#4905)
• Improved docstring for util.random_noise (#5001)
• Improved docstrings for morphology.h_maxima and morphology.h_minima
  (#4929).
• Improved docstring for util.img_as_int (#4888).
• A new example demonstrates interactive exploration of regionprops results
  using the PyData stack (pandas, seaborn) at
  https://scikit-image.org/docs/dev/auto_examples/segmentation/plot_regionprops.html`_
  (#5010).
• Documentation has been added to explain
  how to download example datasets <https://scikit-image.org/docs/dev/install.html#downloading-all-demo-datasets>_
  which are not installed with scikit-image (#4984). Similarly, the contributor
  guide has been updated to mention how to host new datasets in a gitlab
  repository (#4892).
• The benchmarking section of the developer documentation <https://scikit-image.org/docs/dev/contribute.html#benchmarks>_
  has been expanded (#4905).
• Added links to the image.sc forum in example pages (#5094, #5096)
• Added missing datasets to gallery examples (#5116, #5118)
• Add farid filters in all, to populate the documentation (#5128, #5129)
• Proofread gallery example for rank filters. (#5126, #5136)

Improvements

• float32 support for SLIC (#4683), ORB (#4684, #4697), BRIEF (#4685),
  pyramid_gaussian (#4696), Richardson-Lucy deconvolution (#4880)
• In skimage.restoration.richardson_lucy, computations are now done in
  single-precision when the input image is single-precision. This can give a
  substantial performance improvement when working with single precision data.
• Richardson-Lucy deconvolution now has a filter_epsilon keyword argument
  to avoid division by very small numbers (#4823)
• Add default level parameter (max-min) / 2 in measure.find_contours (#4862)
• The performance of the SLIC superpixels algorithm
  (skimage.segmentation.slice) was improved for the case where a mask
  is supplied by the user (#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 by using
  a look-up table (LUT) (#4966).
• measure.label has been accelerated for boolean input images, by using
  scipy.ndimage's implementation for this case (#4945).
• util.apply_parallel now works with multichannel data (#4927).
• skimage.feature.peak_local_max supports now any Minkowski distance.
• We now use sparse cross-correlation to accelerate local thresholding
  functions (#4912)
• morphology.convex_hull_image now uses much less memory by checking hull
  inequalities in sequence (#5020)
• Polygon rasterization is more precise and will no longer potentially exclude
  input vertices. (#5029)
• Add data optional requirements to allow pip install scikit-image[data]
  (#5105, #5111)
• OpenMP support in MSVC (#4924, #5111)
• Restandardize handling of Multi-Image files (#2815, #5132)
• Consistent zoom boundary behavior across SciPy versions (#5131, #5133)

API Changes

• skimage.restoration.richardson_lucy returns a single-precision output
  when the input is single-precision. Prior to this release, double-precision
  was always used. (#4880)
• The default value of threshold_rel in skimage.feature.corner has
  changed from 0.1 to None, which corresponds to letting
  skimage.feature.peak_local_max decide on the default. This is currently
  equivalent to threshold_rel=0.
• In measure.label, the deprecated neighbors parameter has been
  removed. (#4942)
• The image returned by data.camera has changed because of copyright
  issues (#4913).

Bug fixes

• A bug in label2rgb has been fixed when the input image had np.uint8
  dtype (#4661)
• Fixed incorrect implementation of skimage.color.separate_stains (#4725)
• Many bug fixes have been made in peak_local_max (#2592, #4756, #4760,
  #5047)
• Fix bug in random_walker when input labels have negative values (#4771)
• PSF flipping is now correct for Richardson-Lucy deconvolution work in >2D (#4823)
• Fix equalize_adapthist (CLAHE) for clip value 1.0 (#4828)
• For the RANSAC algorithm, improved the case where all data points are
  outliers, which was previously raising an error
  (#4844)
• An error-causing bug has been corrected for the bg_color parameter in
  label2rgb when its value is a string (#4840)
• A normalization bug was fixed in metrics.variation_of_information
  (#4875)
• Euler characteristic property of skimage.measure.regionprops was erroneous
  for 3D objects, since it did not take tunnels into account. A new implementation
  based on integral geometry fixes this bug (#4380).
• In skimage.morphology.selem.rectangle the height argument
  controlled the width and the width argument controlled the height.
  They have been replaced with nrow and ncol. (#4906)
• skimage.segmentation.flood_fill and skimage.segmentation.flood
  now consistently handle negative values for seed_point.
• Segmentation faults in segmentation.flood have been fixed (#4948, #4972)
• A segfault in draw.polygon for the case of 0-d input has been fixed
  (#4943).
• In registration.phase_cross_correlation, a ValueError is raised when
  NaNs are found in the computation (as a result of NaNs in input images).
  Before this fix, an incorrect value could be returned where the input images
  had NaNs (#4886).
• Fix edge filters not respecting padding mode (#4907)
• Use v{} for version tags with pooch (#5104, #5110)
• Fix compilation error in XCode 12 (#5107, #5111)

Deprecations

• The indices argument in skimage.feature.peak_local_max has been
  deprecated. Indices will always be returned. (#4752)
• In skimage.feature.structure_tensor, an order argument has been
  introduced which will default to 'rc' starting in version 0.20. (#4841)
• skimage.feature.structure_tensor_eigvals has been deprecated and will be
  removed in version 0.20. Use skimage.feature.structure_tensor_eigenvalues
  instead.
• The skimage.viewer subpackage and the skivi script have been
  deprecated and will be removed in version 0.20. For interactive visualization
  we recommend using dedicated tools such as napari <https://napari.org>_ or
  plotly <https://plotly.com>_. In a similar vein, the qt and skivi
  plugins of skimage.io have been deprecated
  and will be removed in version 0.20. (#4941, #4954)
• In skimage.morphology.selem.rectangle the arguments width and
  height have been deprecated. Use nrow and ncol instead.
• The explicit setting threshold_rel=0` was removed from the Examples of the following docstrings: skimage.feature.BRIEF, skimage.feature.corner_harris, skimage.feature.corner_shi_tomasi, skimage.feature.corner_foerstner, skimage.feature.corner_fast, skimage.feature.corner_subpix, skimage.feature.corner_peaks, skimage.feature.corner_orientations, and skimage.feature._detect_octave``.
• In skimage.restoration._denoise, the warning regarding
  rescale_sigma=None was removed.
• In skimage.restoration._cycle_spin, the # doctest: +SKIP was removed.

Development process

• Fix #3327: Add functionality for benchmark coverage (#3329)
• Release process notes have been improved. (#4228)
• pyproject.toml has been added to the sdist.
• Build and deploy dev/master documentation using GitHub Actions (#4852)
• Website now deploys itself (#4870)
• build doc on circle ci and link artifact (#4881)
• Benchmarks can now run on older scikit-image commits (#4891)
• Website analytics are tracked using plausible.io and can be visualized on
  https://plausible.io/scikit-image.org (#4893)
• Artifacts for the documentation build are now found in each pull request
  (#4881).
• Documentation source files can now be written in Markdown in addition to
  ReST, thanks to myst (#4863).
• update trove classifiers and tests for Python 3.9 + fix pytest config (#5052)
• fix Azure Pipelines, pytest config, and trove classifiers for Python 3.8 (#5054)
• Moved our testing from Travis to GitHub Actions (#5074)
• We now build our wheels on GitHub Actions on the main repo using
  cibuildwheel. Many thanks to the matplotlib and scikit-learn developers for
  paving the way for us! (#5080)
• Disable Travis-CI builds (#5099, #5111)
• Improvements to CircleCI build: no parallelization and caching) (#5097, #5119)

Other Pull Requests

• Manage iradon input and output data type (#4298)
• random walker: Display a warning when the probability is outsite [0,1] for a given tol (#4631)
• MAINT: remove unused cython file (#4633)
• Forget legacy data dir (#4662)
• Setup longdesc markdown and switch to 0.18dev (#4663)
• Optional pooch dependency (#4666)
• Adding new default values to functions on doc/examples/segmentation/plot_ncut (#4676)
• Reintroduced convert with a strong deprecation warning (#4681)
• In release notes, better describe skimage's relationship to ecosystem (#4689)
• Perform some todo tasks for 0.18 (#4690)
• Perform todo tasks for 0.17! (#4691)
• suppressing warnings from gallery examples (#4692)
• release notes for 0.17.2 (#4702)
• Fix gallery example mentioning deprecated argument (#4706)
• Specify the encoding of files opened in the setup phase (#4713)
• Remove duplicate fused type definition (#4724)
• Blacklist cython version 0.29.18 (#4730)
• Fix CI failures related to conversion of np.floating to dtype (#4731)
• Fix Ci failures related to array ragged input numpy deprecation (#4735)
• Unwrap decorators before resolving link to source (sphinx.ext.linkcode) (#4740)
• Fix plotting error in j-invariant denoising tutorial (#4744)
• Highlight all source lines with HTML doc "source" links (sphinx.ext.linkcode) (#4746)
• Turn checklist boxes into bullet points inside the pull request template (#4747)
• Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max (#4753)
• forbid dask 2.17.0 to fix CI (#4758)
• try to fix ci which is broken because of pyqt5 last version (#4788)
• Remove unused variable in j invariant docs (#4792)
• include all md files in manifest.in (#4793)
• Remove additional "::" to make plot directive work. (#4798)
• Use optipng to compress images/thumbnails in our gallery (#4800)
• Fix runtime warning in blob.py (#4803)
• Add TODO task for sphinx-gallery>=0.9.0 to remove enforced thumbnail_size (#4804)
• Change SSIM code example to use real MSE (#4807)
• Let biomed example load image data with Pooch. (#4809)
• Tweak threshold_otsu error checking - closes #4811 (#4812)
• Ensure assert messages from Cython rank filters are informative (#4815)
• Simplify equivalent_diameter function (#4819)
• DOC: update subpackage descriptions (#4825)
• style: be explicit when stacking arrays (#4826)
• MAINT: import Iterable from collections.abc (Python 3.9 compatibility) (#4834)
• Silence several warnings in the test suite (#4837)
• Silence a few RuntimeWarnings in the test suite (#4838)
• handle color string mapping correctly (#4840)
• DOC: Autoformat docstrings in io.*.py (#4845)
• Update min req for pillow due to CVE-2020-10379 and co. (#4861)
• DOC: First pass at format conversion, rst -> myst (#4863)
• Fixed typo in comment (#4867)
• Alternative wording for install guide PR #4750 (#4871)
• DOC: Clarify condition on unique vertices returned by marching cubes (#4872)
• Remove unmaintained wiki page link in contributor guidelines (#4873)
• new matomo config (#4879)
• Fix Incorrect documentation for skimage.util.img_as_int Issue (#4888)
• Minor edit for proper doc rendering (#4897)
• Changelog back-log (#4898)
• minor refactoring in phase_cross_correlation (#4901)
• Fix draw.circle/disk deprecation message, fixes #4884 (#4908)
• Add versionchanged tag for new opt param in measure.find_contours() (#4909)
• Declare build dependencies (#4920)
• Replace words with racial connotations (#4921)
• Fixes to apply_parallel for functions working with multichannel data (#4927)
• Improve description of h_maxima and h_minima functions (#4928) (#4929)
• CI: Skip doc build for PYTHONOPTIMIZE=2 (#4930)
• MAINT: Remove custom fused type in skimage/morphology/_max_tree.pyx (#4931)
• MAINT: remove numpydoc option, issue fixed in numpydoc 1.0 (#4932)
• modify development version string to allow use with NumpyVersion (#4947)
• CI: Add verbose option to avoid travis timeout for OSX install script (#4956)
• Fix CI: ban sphinx-gallery 0.8.0 (#4960)
• Alias for data.chelsea: data.cat() (#4962)
• Fix typo. (#4963)
• CI: Use Travis wait improved to avoid timeout for OSX builds (#4965)
• Small enhancement in "Contour finding" example: Removed unused variable n (#4967)
• MAINT: remove unused imports (#4968)
• MAINT: Remove conditional import on networkx (#4970)
• forbid latest version of pyqt (#4973)
• Remove warnings/explicit settings on feature, restoration (#4974)
• Docstring improvements for label and regionprops_label (#4983)
• try to fix timeout problem with circleci (#4986)
• improve Euler number example (#4989)
• [website] Standardize Documentation index page. (#4990)
• Proofread INSTALL file. (#4991)
• Catch leftover typos in INSTALL file. (#4992)
• Let tifffile.imread handle additional keyword arguments (#4997)
• Update docstring for random_noise function (#5001)
• Update sphinx mapping for sklearn and numpy (#5003)
• Update docstring slic superpixels (#5014)
• Bump numpy versions to match scipy (kinda) (#5016)
• Fix usage of numpy.pad for old versions of numpy (#5017)
• [MRG] Update documentation to new data.camera() (#5018)
• bumped plotly requirement for docs (#5021)
• Fix IndexError when calling hough_line_peaks with too few angles (#5024)
• Code simplification after latest numpy bump (#5027)
• Fixes broken link to CODE_OF_CONDUCT.md (#5030)
• Specify whether core dev should merge right after second approving review. (#5040)
• Update pytest configuration to include test_ functions (#5044)
• MAINT Build fix for pyodide (#5059)
• reduce OSX build time so that Travis is happy (#5067)
• DOC: document the normalized kernel in prewitt_h, prewitt_v (#5076)
• Some minor tweaks to CI (#5079)
• removed usage of numpy's private functions from util.arraycrop (#5081)
• peak_local_max: remove deprecated indices argument from examples (#5082)
• Replace np.bool, np.float, and np.int with bool, float, and int (#5103, #5108)
• change plausible script to track outbound links (#5115, #5123)
• Remove Python 3.6 support (#5117, #5125)
• Optimize ensure_spacing (#5062, #5135)

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

A warm thank you to all contributors who added to this release. A fraction of contributors were first-time contributors to open source and a much larger fraction first-time contributors to scikit-image. It's a great feeling for maintainers to welcome new contributors, and the diversity of scikit-image contributors is surely a big strength of the package.

• Abhishek Arya
• Abhishek Patil
• Alexandre de Siqueira
• Ben Nathanson
• Cameron Blocker
• Chris Roat
• Christoph Gohlke
• Clement Ng
• Corey Harris
• David McMahon
• David Mellert
• Devi Sandeep
• Egor Panfilov
• Emmanuelle Gouillart
• François Boulogne
• Genevieve Buckley
• Gregory R. Lee
• Harry Kwon
• iofall (cedarfall)
• Jan Funke
• Juan Nunez-Iglesias
• Julian Gilbey
• Julien Jerphanion
• kalpana
• kolibril13 (kolibril13)
• Kushaan Gupta
• Lars Grüter
• Marianne Corvellec
• Mark Harfouche
• Marvin Albert
• Matthias Bussonnier
• Max Frei
• Nathan
• neeraj3029 (neeraj3029)
• Nick
• notmatthancock (matt)
• OGordon100 (OGordon100)
• Owen Solberg
• Riadh Fezzani
• Robert Haase
• Roman Yurchak
• Ronak Sharma
• Ross Barnowski
• Ruby Werman
• ryanlu41 (ryanlu41)
• Sebastian Wallkötter
• Shyam Saladi
• Stefan van der Walt
• Terence Honles
• Volker Hilsenstein
• Wendy Mak
• Yogendra Sharma

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

• Abhishek Arya
• Abhishek Patil
• Alexandre de Siqueira
• Ben Nathanson
• Chris Roat
• Clement Ng
• Corey Harris
• Cris Luengo
• David Mellert
• Egor Panfilov
• Emmanuelle Gouillart
• François Boulogne
• Gregory R. Lee
• Harry Kwon
• Jan Funke
• Juan Nunez-Iglesias
• Julien Jerphanion
• kalpana
• Kushaan Gupta
• Lars Grüter
• Marianne Corvellec
• Mark Harfouche
• Marvin Albert
• neeraj3029
• Nick
• OGordon100
• Riadh Fezzani
• Robert Haase
• Ross Barnowski
• Ruby Werman
• ryanlu41
• Scott Trinkle
• Sebastian Wallkötter
• Stanley_Wang
• Stefan van der Walt
• Steven Brown
• Stuart Mumford
• Terence Honles
• Volker Hilsenstein
• Wendy Mak