scikit-image/scikit-image
### [`v0.18.1`](https://togithub.com/scikit-image/scikit-image/releases/v0.18.1)
[Compare Source](https://togithub.com/scikit-image/scikit-image/compare/v0.18.0...v0.18.1)
# scikit-image 0.18.1
This is a bug fix release and contains the following two bug fixes:
- Fix indexing error for labelling in large (>2GB) arrays ([#5143](https://togithub.com/scikit-image/scikit-image/issues/5143), [#5151](https://togithub.com/scikit-image/scikit-image/issues/5151))
- Only use retry_if_failed with recent pooch ([#5148](https://togithub.com/scikit-image/scikit-image/issues/5148))
See below for the new features and API changes in 0.18.0.
# 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
`\_: Python 3.7 or
newer is required to run this version.
For more information, examples, and documentation, please visit our website:
## New Features
- Add the iterative Lucas-Kanade (iLK) optical flow method ([#4161](https://togithub.com/scikit-image/scikit-image/issues/4161))
- Add Feret diameter in region properties ([#4379](https://togithub.com/scikit-image/scikit-image/issues/4379), [#4820](https://togithub.com/scikit-image/scikit-image/issues/4820))
- Add functions to compute Euler number and Crofton perimeter estimation ([#4380](https://togithub.com/scikit-image/scikit-image/issues/4380))
- Add a function to compute the Hausdorff distance ([#4382](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4739))
- Add a new function `segmentation.expand_labels` to dilate labels while
preventing overlap ([#4795](https://togithub.com/scikit-image/scikit-image/issues/4795))
- It is now possible to pass extra measurement functions to
`measure.regionprops` and `regionprops_table` ([#4810](https://togithub.com/scikit-image/scikit-image/issues/4810))
- Add rolling ball algorithm for background subtraction ([#4851](https://togithub.com/scikit-image/scikit-image/issues/4851))
- New sample images have been added in the `data` subpackage: `data.eagle`
([#4922](https://togithub.com/scikit-image/scikit-image/issues/4922)), `data.human_mitosis` ([#4939](https://togithub.com/scikit-image/scikit-image/issues/4939)), `data.cells3d` ([#4951](https://togithub.com/scikit-image/scikit-image/issues/4951)), and
`data.vortex` ([#5041](https://togithub.com/scikit-image/scikit-image/issues/5041)). Also note that the image for `data.camera` has
been changed due to copyright issues ([#4913](https://togithub.com/scikit-image/scikit-image/issues/4913)).
- `skimage.feature.structure_tensor` now supports 3D (and nD) images as input
([#5002](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/5006))
- `measure.regionprops` now supports multichannel intensity images ([#5037](https://togithub.com/scikit-image/scikit-image/issues/5037))
## Documentation
- Add an example to the flood fill tutorial ([#4619](https://togithub.com/scikit-image/scikit-image/issues/4619))
- Docstring enhancements for marching cubes and find_contours ([#4641](https://togithub.com/scikit-image/scikit-image/issues/4641))
- A new tutorial presenting a cell biology example has been added to the
gallery ([#4648](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4723))
- Add versionadded for new scalar type support for "scale" param in
`transform.AffineTransform` ([#4733](https://togithub.com/scikit-image/scikit-image/issues/4733))
- New tutorial on `visualizing 3D data `\_ ([#4850](https://togithub.com/scikit-image/scikit-image/issues/4850))
- Add example for 3D adaptive histogram equalization (AHE) ([#4658](https://togithub.com/scikit-image/scikit-image/issues/4658))
- Automatic formatting of docstrings for improved consistency ([#4849](https://togithub.com/scikit-image/scikit-image/issues/4849))
- Improved docstring for `rgb2lab` ([#4839](https://togithub.com/scikit-image/scikit-image/issues/4839)) and `marching_cubes` ([#4846](https://togithub.com/scikit-image/scikit-image/issues/4846))
- Improved docstring for `measure.marching_cubes`, mentioning how to decimate a
mesh using mayavi ([#4846](https://togithub.com/scikit-image/scikit-image/issues/4846))
- Document how to contribute a gallery example. ([#4857](https://togithub.com/scikit-image/scikit-image/issues/4857))
- Fix and improve entropy example ([#4904](https://togithub.com/scikit-image/scikit-image/issues/4904))
- expand the benchmarking section of the developer docs ([#4905](https://togithub.com/scikit-image/scikit-image/issues/4905))
- Improved docstring for `util.random_noise` ([#5001](https://togithub.com/scikit-image/scikit-image/issues/5001))
- Improved docstrings for `morphology.h_maxima` and `morphology.h_minima`
([#4929](https://togithub.com/scikit-image/scikit-image/issues/4929)).
- Improved docstring for `util.img_as_int` ([#4888](https://togithub.com/scikit-image/scikit-image/issues/4888)).
- A new example demonstrates interactive exploration of regionprops results
using the PyData stack (pandas, seaborn) at
\`\_
([#5010](https://togithub.com/scikit-image/scikit-image/issues/5010)).
- Documentation has been added to explain
`how to download example datasets `\_
which are not installed with scikit-image ([#4984](https://togithub.com/scikit-image/scikit-image/issues/4984)). Similarly, the contributor
guide has been updated to mention how to host new datasets in a gitlab
repository ([#4892](https://togithub.com/scikit-image/scikit-image/issues/4892)).
- The `benchmarking section of the developer documentation `\_
has been expanded ([#4905](https://togithub.com/scikit-image/scikit-image/issues/4905)).
- Added links to the image.sc forum in example pages ([#5094](https://togithub.com/scikit-image/scikit-image/issues/5094), [#5096](https://togithub.com/scikit-image/scikit-image/issues/5096))
- Added missing datasets to gallery examples ([#5116](https://togithub.com/scikit-image/scikit-image/issues/5116), [#5118](https://togithub.com/scikit-image/scikit-image/issues/5118))
- Add farid filters in **all**, to populate the documentation ([#5128](https://togithub.com/scikit-image/scikit-image/issues/5128), [#5129](https://togithub.com/scikit-image/scikit-image/issues/5129))
- Proofread gallery example for rank filters. ([#5126](https://togithub.com/scikit-image/scikit-image/issues/5126), [#5136](https://togithub.com/scikit-image/scikit-image/issues/5136))
## Improvements
- float32 support for SLIC ([#4683](https://togithub.com/scikit-image/scikit-image/issues/4683)), ORB ([#4684](https://togithub.com/scikit-image/scikit-image/issues/4684), [#4697](https://togithub.com/scikit-image/scikit-image/issues/4697)), BRIEF ([#4685](https://togithub.com/scikit-image/scikit-image/issues/4685)),
`pyramid_gaussian` ([#4696](https://togithub.com/scikit-image/scikit-image/issues/4696)), Richardson-Lucy deconvolution ([#4880](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4823))
- Add default level parameter (max-min) / 2 in `measure.find_contours` ([#4862](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4966)).
- `measure.label` has been accelerated for boolean input images, by using
`scipy.ndimage`'s implementation for this case ([#4945](https://togithub.com/scikit-image/scikit-image/issues/4945)).
- `util.apply_parallel` now works with multichannel data ([#4927](https://togithub.com/scikit-image/scikit-image/issues/4927)).
- `skimage.feature.peak_local_max` supports now any Minkowski distance.
- We now use sparse cross-correlation to accelerate local thresholding
functions ([#4912](https://togithub.com/scikit-image/scikit-image/issues/4912))
- `morphology.convex_hull_image` now uses much less memory by checking hull
inequalities in sequence ([#5020](https://togithub.com/scikit-image/scikit-image/issues/5020))
- Polygon rasterization is more precise and will no longer potentially exclude
input vertices. ([#5029](https://togithub.com/scikit-image/scikit-image/issues/5029))
- Add data optional requirements to allow pip install scikit-image[data]
([#5105](https://togithub.com/scikit-image/scikit-image/issues/5105), [#5111](https://togithub.com/scikit-image/scikit-image/issues/5111))
- OpenMP support in MSVC ([#4924](https://togithub.com/scikit-image/scikit-image/issues/4924), [#5111](https://togithub.com/scikit-image/scikit-image/issues/5111))
- Restandardize handling of Multi-Image files ([#2815](https://togithub.com/scikit-image/scikit-image/issues/2815), [#5132](https://togithub.com/scikit-image/scikit-image/issues/5132))
- Consistent zoom boundary behavior across SciPy versions ([#5131](https://togithub.com/scikit-image/scikit-image/issues/5131), [#5133](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4942))
- The image returned by `data.camera` has changed because of copyright
issues ([#4913](https://togithub.com/scikit-image/scikit-image/issues/4913)).
## Bug fixes
- A bug in `label2rgb` has been fixed when the input image had np.uint8
dtype ([#4661](https://togithub.com/scikit-image/scikit-image/issues/4661))
- Fixed incorrect implementation of `skimage.color.separate_stains` ([#4725](https://togithub.com/scikit-image/scikit-image/issues/4725))
- Many bug fixes have been made in `peak_local_max` ([#2592](https://togithub.com/scikit-image/scikit-image/issues/2592), [#4756](https://togithub.com/scikit-image/scikit-image/issues/4756), [#4760](https://togithub.com/scikit-image/scikit-image/issues/4760),
[#5047](https://togithub.com/scikit-image/scikit-image/issues/5047))
- Fix bug in `random_walker` when input labels have negative values ([#4771](https://togithub.com/scikit-image/scikit-image/issues/4771))
- PSF flipping is now correct for Richardson-Lucy deconvolution work in >2D ([#4823](https://togithub.com/scikit-image/scikit-image/issues/4823))
- Fix equalize_adapthist (CLAHE) for clip value 1.0 ([#4828](https://togithub.com/scikit-image/scikit-image/issues/4828))
- For the RANSAC algorithm, improved the case where all data points are
outliers, which was previously raising an error
([#4844](https://togithub.com/scikit-image/scikit-image/issues/4844))
- An error-causing bug has been corrected for the `bg_color` parameter in
`label2rgb` when its value is a string ([#4840](https://togithub.com/scikit-image/scikit-image/issues/4840))
- A normalization bug was fixed in `metrics.variation_of_information`
([#4875](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4948), [#4972](https://togithub.com/scikit-image/scikit-image/issues/4972))
- A segfault in `draw.polygon` for the case of 0-d input has been fixed
([#4943](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4886)).
- Fix edge filters not respecting padding mode ([#4907](https://togithub.com/scikit-image/scikit-image/issues/4907))
- Use v{} for version tags with pooch ([#5104](https://togithub.com/scikit-image/scikit-image/issues/5104), [#5110](https://togithub.com/scikit-image/scikit-image/issues/5110))
- Fix compilation error in XCode 12 ([#5107](https://togithub.com/scikit-image/scikit-image/issues/5107), [#5111](https://togithub.com/scikit-image/scikit-image/issues/5111))
## Deprecations
- The `indices` argument in `skimage.feature.peak_local_max` has been
deprecated. Indices will always be returned. ([#4752](https://togithub.com/scikit-image/scikit-image/issues/4752))
- In `skimage.feature.structure_tensor`, an `order` argument has been
introduced which will default to 'rc' starting in version 0.20. ([#4841](https://togithub.com/scikit-image/scikit-image/issues/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 `_ or
`plotly `_. In a similar vein, the `qt` and `skivi`
plugins of `skimage.io` have been deprecated
and will be removed in version 0.20. ([#4941](https://togithub.com/scikit-image/scikit-image/issues/4941), [#4954](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/3327): Add functionality for benchmark coverage ([#3329](https://togithub.com/scikit-image/scikit-image/issues/3329))
- Release process notes have been improved. ([#4228](https://togithub.com/scikit-image/scikit-image/issues/4228))
- `pyproject.toml` has been added to the sdist.
- Build and deploy dev/master documentation using GitHub Actions ([#4852](https://togithub.com/scikit-image/scikit-image/issues/4852))
- Website now deploys itself ([#4870](https://togithub.com/scikit-image/scikit-image/issues/4870))
- build doc on circle ci and link artifact ([#4881](https://togithub.com/scikit-image/scikit-image/issues/4881))
- Benchmarks can now run on older scikit-image commits ([#4891](https://togithub.com/scikit-image/scikit-image/issues/4891))
- Website analytics are tracked using plausible.io and can be visualized on
([#4893](https://togithub.com/scikit-image/scikit-image/issues/4893))
- Artifacts for the documentation build are now found in each pull request
([#4881](https://togithub.com/scikit-image/scikit-image/issues/4881)).
- Documentation source files can now be written in Markdown in addition to
ReST, thanks to `myst` ([#4863](https://togithub.com/scikit-image/scikit-image/issues/4863)).
- update trove classifiers and tests for Python 3.9 + fix pytest config ([#5052](https://togithub.com/scikit-image/scikit-image/issues/5052))
- fix Azure Pipelines, pytest config, and trove classifiers for Python 3.8 ([#5054](https://togithub.com/scikit-image/scikit-image/issues/5054))
- Moved our testing from Travis to GitHub Actions ([#5074](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/5080))
- Disable Travis-CI builds ([#5099](https://togithub.com/scikit-image/scikit-image/issues/5099), [#5111](https://togithub.com/scikit-image/scikit-image/issues/5111))
- Improvements to CircleCI build: no parallelization and caching) ([#5097](https://togithub.com/scikit-image/scikit-image/issues/5097), [#5119](https://togithub.com/scikit-image/scikit-image/issues/5119))
## Other Pull Requests
- Manage iradon input and output data type ([#4298](https://togithub.com/scikit-image/scikit-image/issues/4298))
- random walker: Display a warning when the probability is outsite [0,1] for a given tol ([#4631](https://togithub.com/scikit-image/scikit-image/issues/4631))
- MAINT: remove unused cython file ([#4633](https://togithub.com/scikit-image/scikit-image/issues/4633))
- Forget legacy data dir ([#4662](https://togithub.com/scikit-image/scikit-image/issues/4662))
- Setup longdesc markdown and switch to 0.18dev ([#4663](https://togithub.com/scikit-image/scikit-image/issues/4663))
- Optional pooch dependency ([#4666](https://togithub.com/scikit-image/scikit-image/issues/4666))
- Adding new default values to functions on doc/examples/segmentation/plot_ncut ([#4676](https://togithub.com/scikit-image/scikit-image/issues/4676))
- Reintroduced convert with a strong deprecation warning ([#4681](https://togithub.com/scikit-image/scikit-image/issues/4681))
- In release notes, better describe skimage's relationship to ecosystem ([#4689](https://togithub.com/scikit-image/scikit-image/issues/4689))
- Perform some todo tasks for 0.18 ([#4690](https://togithub.com/scikit-image/scikit-image/issues/4690))
- Perform todo tasks for 0.17! ([#4691](https://togithub.com/scikit-image/scikit-image/issues/4691))
- suppressing warnings from gallery examples ([#4692](https://togithub.com/scikit-image/scikit-image/issues/4692))
- release notes for 0.17.2 ([#4702](https://togithub.com/scikit-image/scikit-image/issues/4702))
- Fix gallery example mentioning deprecated argument ([#4706](https://togithub.com/scikit-image/scikit-image/issues/4706))
- Specify the encoding of files opened in the setup phase ([#4713](https://togithub.com/scikit-image/scikit-image/issues/4713))
- Remove duplicate fused type definition ([#4724](https://togithub.com/scikit-image/scikit-image/issues/4724))
- Blacklist cython version 0.29.18 ([#4730](https://togithub.com/scikit-image/scikit-image/issues/4730))
- Fix CI failures related to conversion of np.floating to dtype ([#4731](https://togithub.com/scikit-image/scikit-image/issues/4731))
- Fix Ci failures related to array ragged input numpy deprecation ([#4735](https://togithub.com/scikit-image/scikit-image/issues/4735))
- Unwrap decorators before resolving link to source (sphinx.ext.linkcode) ([#4740](https://togithub.com/scikit-image/scikit-image/issues/4740))
- Fix plotting error in j-invariant denoising tutorial ([#4744](https://togithub.com/scikit-image/scikit-image/issues/4744))
- Highlight all source lines with HTML doc "source" links (sphinx.ext.linkcode) ([#4746](https://togithub.com/scikit-image/scikit-image/issues/4746))
- Turn checklist boxes into bullet points inside the pull request template ([#4747](https://togithub.com/scikit-image/scikit-image/issues/4747))
- Deprecate (min_distance < 1) and (footprint.size < 2) in peak_local_max ([#4753](https://togithub.com/scikit-image/scikit-image/issues/4753))
- forbid dask 2.17.0 to fix CI ([#4758](https://togithub.com/scikit-image/scikit-image/issues/4758))
- try to fix ci which is broken because of pyqt5 last version ([#4788](https://togithub.com/scikit-image/scikit-image/issues/4788))
- Remove unused variable in j invariant docs ([#4792](https://togithub.com/scikit-image/scikit-image/issues/4792))
- include all md files in manifest.in ([#4793](https://togithub.com/scikit-image/scikit-image/issues/4793))
- Remove additional "::" to make plot directive work. ([#4798](https://togithub.com/scikit-image/scikit-image/issues/4798))
- Use optipng to compress images/thumbnails in our gallery ([#4800](https://togithub.com/scikit-image/scikit-image/issues/4800))
- Fix runtime warning in blob.py ([#4803](https://togithub.com/scikit-image/scikit-image/issues/4803))
- Add TODO task for sphinx-gallery>=0.9.0 to remove enforced thumbnail_size ([#4804](https://togithub.com/scikit-image/scikit-image/issues/4804))
- Change SSIM code example to use real MSE ([#4807](https://togithub.com/scikit-image/scikit-image/issues/4807))
- Let biomed example load image data with Pooch. ([#4809](https://togithub.com/scikit-image/scikit-image/issues/4809))
- Tweak threshold_otsu error checking - closes [#4811](https://togithub.com/scikit-image/scikit-image/issues/4811) ([#4812](https://togithub.com/scikit-image/scikit-image/issues/4812))
- Ensure assert messages from Cython rank filters are informative ([#4815](https://togithub.com/scikit-image/scikit-image/issues/4815))
- Simplify equivalent_diameter function ([#4819](https://togithub.com/scikit-image/scikit-image/issues/4819))
- DOC: update subpackage descriptions ([#4825](https://togithub.com/scikit-image/scikit-image/issues/4825))
- style: be explicit when stacking arrays ([#4826](https://togithub.com/scikit-image/scikit-image/issues/4826))
- MAINT: import Iterable from collections.abc (Python 3.9 compatibility) ([#4834](https://togithub.com/scikit-image/scikit-image/issues/4834))
- Silence several warnings in the test suite ([#4837](https://togithub.com/scikit-image/scikit-image/issues/4837))
- Silence a few RuntimeWarnings in the test suite ([#4838](https://togithub.com/scikit-image/scikit-image/issues/4838))
- handle color string mapping correctly ([#4840](https://togithub.com/scikit-image/scikit-image/issues/4840))
- DOC: Autoformat docstrings in `io.*.py` ([#4845](https://togithub.com/scikit-image/scikit-image/issues/4845))
- Update min req for pillow due to CVE-2020-10379 and co. ([#4861](https://togithub.com/scikit-image/scikit-image/issues/4861))
- DOC: First pass at format conversion, rst -> myst ([#4863](https://togithub.com/scikit-image/scikit-image/issues/4863))
- Fixed typo in comment ([#4867](https://togithub.com/scikit-image/scikit-image/issues/4867))
- Alternative wording for install guide PR [#4750](https://togithub.com/scikit-image/scikit-image/issues/4750) ([#4871](https://togithub.com/scikit-image/scikit-image/issues/4871))
- DOC: Clarify condition on unique vertices returned by marching cubes ([#4872](https://togithub.com/scikit-image/scikit-image/issues/4872))
- Remove unmaintained wiki page link in contributor guidelines ([#4873](https://togithub.com/scikit-image/scikit-image/issues/4873))
- new matomo config ([#4879](https://togithub.com/scikit-image/scikit-image/issues/4879))
- Fix Incorrect documentation for skimage.util.img_as_int Issue ([#4888](https://togithub.com/scikit-image/scikit-image/issues/4888))
- Minor edit for proper doc rendering ([#4897](https://togithub.com/scikit-image/scikit-image/issues/4897))
- Changelog back-log ([#4898](https://togithub.com/scikit-image/scikit-image/issues/4898))
- minor refactoring in phase_cross_correlation ([#4901](https://togithub.com/scikit-image/scikit-image/issues/4901))
- Fix draw.circle/disk deprecation message, fixes [#4884](https://togithub.com/scikit-image/scikit-image/issues/4884) ([#4908](https://togithub.com/scikit-image/scikit-image/issues/4908))
- Add versionchanged tag for new opt param in measure.find_contours() ([#4909](https://togithub.com/scikit-image/scikit-image/issues/4909))
- Declare build dependencies ([#4920](https://togithub.com/scikit-image/scikit-image/issues/4920))
- Replace words with racial connotations ([#4921](https://togithub.com/scikit-image/scikit-image/issues/4921))
- Fixes to apply_parallel for functions working with multichannel data ([#4927](https://togithub.com/scikit-image/scikit-image/issues/4927))
- Improve description of h_maxima and h_minima functions ([#4928](https://togithub.com/scikit-image/scikit-image/issues/4928)) ([#4929](https://togithub.com/scikit-image/scikit-image/issues/4929))
- CI: Skip doc build for PYTHONOPTIMIZE=2 ([#4930](https://togithub.com/scikit-image/scikit-image/issues/4930))
- MAINT: Remove custom fused type in skimage/morphology/\_max_tree.pyx ([#4931](https://togithub.com/scikit-image/scikit-image/issues/4931))
- MAINT: remove numpydoc option, issue fixed in numpydoc 1.0 ([#4932](https://togithub.com/scikit-image/scikit-image/issues/4932))
- modify development version string to allow use with NumpyVersion ([#4947](https://togithub.com/scikit-image/scikit-image/issues/4947))
- CI: Add verbose option to avoid travis timeout for OSX install script ([#4956](https://togithub.com/scikit-image/scikit-image/issues/4956))
- Fix CI: ban sphinx-gallery 0.8.0 ([#4960](https://togithub.com/scikit-image/scikit-image/issues/4960))
- Alias for data.chelsea: data.cat() ([#4962](https://togithub.com/scikit-image/scikit-image/issues/4962))
- Fix typo. ([#4963](https://togithub.com/scikit-image/scikit-image/issues/4963))
- CI: Use Travis wait improved to avoid timeout for OSX builds ([#4965](https://togithub.com/scikit-image/scikit-image/issues/4965))
- Small enhancement in "Contour finding" example: Removed unused variable n ([#4967](https://togithub.com/scikit-image/scikit-image/issues/4967))
- MAINT: remove unused imports ([#4968](https://togithub.com/scikit-image/scikit-image/issues/4968))
- MAINT: Remove conditional import on networkx ([#4970](https://togithub.com/scikit-image/scikit-image/issues/4970))
- forbid latest version of pyqt ([#4973](https://togithub.com/scikit-image/scikit-image/issues/4973))
- Remove warnings/explicit settings on feature, restoration ([#4974](https://togithub.com/scikit-image/scikit-image/issues/4974))
- Docstring improvements for label and regionprops_label ([#4983](https://togithub.com/scikit-image/scikit-image/issues/4983))
- try to fix timeout problem with circleci ([#4986](https://togithub.com/scikit-image/scikit-image/issues/4986))
- improve Euler number example ([#4989](https://togithub.com/scikit-image/scikit-image/issues/4989))
- [website] Standardize Documentation index page. ([#4990](https://togithub.com/scikit-image/scikit-image/issues/4990))
- Proofread INSTALL file. ([#4991](https://togithub.com/scikit-image/scikit-image/issues/4991))
- Catch leftover typos in INSTALL file. ([#4992](https://togithub.com/scikit-image/scikit-image/issues/4992))
- Let tifffile.imread handle additional keyword arguments ([#4997](https://togithub.com/scikit-image/scikit-image/issues/4997))
- Update docstring for random_noise function ([#5001](https://togithub.com/scikit-image/scikit-image/issues/5001))
- Update sphinx mapping for sklearn and numpy ([#5003](https://togithub.com/scikit-image/scikit-image/issues/5003))
- Update docstring slic superpixels ([#5014](https://togithub.com/scikit-image/scikit-image/issues/5014))
- Bump numpy versions to match scipy (kinda) ([#5016](https://togithub.com/scikit-image/scikit-image/issues/5016))
- Fix usage of numpy.pad for old versions of numpy ([#5017](https://togithub.com/scikit-image/scikit-image/issues/5017))
- [MRG] Update documentation to new data.camera() ([#5018](https://togithub.com/scikit-image/scikit-image/issues/5018))
- bumped plotly requirement for docs ([#5021](https://togithub.com/scikit-image/scikit-image/issues/5021))
- Fix IndexError when calling hough_line_peaks with too few angles ([#5024](https://togithub.com/scikit-image/scikit-image/issues/5024))
- Code simplification after latest numpy bump ([#5027](https://togithub.com/scikit-image/scikit-image/issues/5027))
- Fixes broken link to CODE_OF_CONDUCT.md ([#5030](https://togithub.com/scikit-image/scikit-image/issues/5030))
- Specify whether core dev should merge right after second approving review. ([#5040](https://togithub.com/scikit-image/scikit-image/issues/5040))
- Update pytest configuration to include `test_` functions ([#5044](https://togithub.com/scikit-image/scikit-image/issues/5044))
- MAINT Build fix for pyodide ([#5059](https://togithub.com/scikit-image/scikit-image/issues/5059))
- reduce OSX build time so that Travis is happy ([#5067](https://togithub.com/scikit-image/scikit-image/issues/5067))
- DOC: document the normalized kernel in prewitt_h, prewitt_v ([#5076](https://togithub.com/scikit-image/scikit-image/issues/5076))
- Some minor tweaks to CI ([#5079](https://togithub.com/scikit-image/scikit-image/issues/5079))
- removed usage of numpy's private functions from util.arraycrop ([#5081](https://togithub.com/scikit-image/scikit-image/issues/5081))
- peak_local_max: remove deprecated `indices` argument from examples ([#5082](https://togithub.com/scikit-image/scikit-image/issues/5082))
- Replace np.bool, np.float, and np.int with bool, float, and int ([#5103](https://togithub.com/scikit-image/scikit-image/issues/5103), [#5108](https://togithub.com/scikit-image/scikit-image/issues/5108))
- change plausible script to track outbound links ([#5115](https://togithub.com/scikit-image/scikit-image/issues/5115), [#5123](https://togithub.com/scikit-image/scikit-image/issues/5123))
- Remove Python 3.6 support ([#5117](https://togithub.com/scikit-image/scikit-image/issues/5117), [#5125](https://togithub.com/scikit-image/scikit-image/issues/5125))
- Optimize ensure_spacing ([#5062](https://togithub.com/scikit-image/scikit-image/issues/5062), [#5135](https://togithub.com/scikit-image/scikit-image/issues/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
### [`v0.18.0`](https://togithub.com/scikit-image/scikit-image/releases/v0.18.0)
[Compare Source](https://togithub.com/scikit-image/scikit-image/compare/v0.17.2...v0.18.0)
# 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
`\_: Python 3.7 or
newer is required to run this version.
For more information, examples, and documentation, please visit our website:
## New Features
- Add the iterative Lucas-Kanade (iLK) optical flow method ([#4161](https://togithub.com/scikit-image/scikit-image/issues/4161))
- Add Feret diameter in region properties ([#4379](https://togithub.com/scikit-image/scikit-image/issues/4379), [#4820](https://togithub.com/scikit-image/scikit-image/issues/4820))
- Add functions to compute Euler number and Crofton perimeter estimation ([#4380](https://togithub.com/scikit-image/scikit-image/issues/4380))
- Add a function to compute the Hausdorff distance ([#4382](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4739))
- Add a new function `segmentation.expand_labels` to dilate labels while
preventing overlap ([#4795](https://togithub.com/scikit-image/scikit-image/issues/4795))
- It is now possible to pass extra measurement functions to
`measure.regionprops` and `regionprops_table` ([#4810](https://togithub.com/scikit-image/scikit-image/issues/4810))
- Add rolling ball algorithm for background subtraction ([#4851](https://togithub.com/scikit-image/scikit-image/issues/4851))
- New sample images have been added in the `data` subpackage: `data.eagle`
([#4922](https://togithub.com/scikit-image/scikit-image/issues/4922)), `data.human_mitosis` ([#4939](https://togithub.com/scikit-image/scikit-image/issues/4939)), `data.cells3d` ([#4951](https://togithub.com/scikit-image/scikit-image/issues/4951)), and
`data.vortex` ([#5041](https://togithub.com/scikit-image/scikit-image/issues/5041)). Also note that the image for `data.camera` has
been changed due to copyright issues ([#4913](https://togithub.com/scikit-image/scikit-image/issues/4913)).
- `skimage.feature.structure_tensor` now supports 3D (and nD) images as input
([#5002](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/5006))
- `measure.regionprops` now supports multichannel intensity images ([#5037](https://togithub.com/scikit-image/scikit-image/issues/5037))
## Documentation
- Add an example to the flood fill tutorial ([#4619](https://togithub.com/scikit-image/scikit-image/issues/4619))
- Docstring enhancements for marching cubes and find_contours ([#4641](https://togithub.com/scikit-image/scikit-image/issues/4641))
- A new tutorial presenting a cell biology example has been added to the
gallery ([#4648](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4723))
- Add versionadded for new scalar type support for "scale" param in
`transform.AffineTransform` ([#4733](https://togithub.com/scikit-image/scikit-image/issues/4733))
- New tutorial on `visualizing 3D data `\_ ([#4850](https://togithub.com/scikit-image/scikit-image/issues/4850))
- Add example for 3D adaptive histogram equalization (AHE) ([#4658](https://togithub.com/scikit-image/scikit-image/issues/4658))
- Automatic formatting of docstrings for improved consistency ([#4849](https://togithub.com/scikit-image/scikit-image/issues/4849))
- Improved docstring for `rgb2lab` ([#4839](https://togithub.com/scikit-image/scikit-image/issues/4839)) and `marching_cubes` ([#4846](https://togithub.com/scikit-image/scikit-image/issues/4846))
- Improved docstring for `measure.marching_cubes`, mentioning how to decimate a
mesh using mayavi ([#4846](https://togithub.com/scikit-image/scikit-image/issues/4846))
- Document how to contribute a gallery example. ([#4857](https://togithub.com/scikit-image/scikit-image/issues/4857))
- Fix and improve entropy example ([#4904](https://togithub.com/scikit-image/scikit-image/issues/4904))
- expand the benchmarking section of the developer docs ([#4905](https://togithub.com/scikit-image/scikit-image/issues/4905))
- Improved docstring for `util.random_noise` ([#5001](https://togithub.com/scikit-image/scikit-image/issues/5001))
- Improved docstrings for `morphology.h_maxima` and `morphology.h_minima`
([#4929](https://togithub.com/scikit-image/scikit-image/issues/4929)).
- Improved docstring for `util.img_as_int` ([#4888](https://togithub.com/scikit-image/scikit-image/issues/4888)).
- A new example demonstrates interactive exploration of regionprops results
using the PyData stack (pandas, seaborn) at
\`\_
([#5010](https://togithub.com/scikit-image/scikit-image/issues/5010)).
- Documentation has been added to explain
`how to download example datasets `\_
which are not installed with scikit-image ([#4984](https://togithub.com/scikit-image/scikit-image/issues/4984)). Similarly, the contributor
guide has been updated to mention how to host new datasets in a gitlab
repository ([#4892](https://togithub.com/scikit-image/scikit-image/issues/4892)).
- The `benchmarking section of the developer documentation `\_
has been expanded ([#4905](https://togithub.com/scikit-image/scikit-image/issues/4905)).
- Added links to the image.sc forum in example pages ([#5094](https://togithub.com/scikit-image/scikit-image/issues/5094), [#5096](https://togithub.com/scikit-image/scikit-image/issues/5096))
- Added missing datasets to gallery examples ([#5116](https://togithub.com/scikit-image/scikit-image/issues/5116), [#5118](https://togithub.com/scikit-image/scikit-image/issues/5118))
- Add farid filters in **all**, to populate the documentation ([#5128](https://togithub.com/scikit-image/scikit-image/issues/5128), [#5129](https://togithub.com/scikit-image/scikit-image/issues/5129))
- Proofread gallery example for rank filters. ([#5126](https://togithub.com/scikit-image/scikit-image/issues/5126), [#5136](https://togithub.com/scikit-image/scikit-image/issues/5136))
## Improvements
- float32 support for SLIC ([#4683](https://togithub.com/scikit-image/scikit-image/issues/4683)), ORB ([#4684](https://togithub.com/scikit-image/scikit-image/issues/4684), [#4697](https://togithub.com/scikit-image/scikit-image/issues/4697)), BRIEF ([#4685](https://togithub.com/scikit-image/scikit-image/issues/4685)),
`pyramid_gaussian` ([#4696](https://togithub.com/scikit-image/scikit-image/issues/4696)), Richardson-Lucy deconvolution ([#4880](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4823))
- Add default level parameter (max-min) / 2 in `measure.find_contours` ([#4862](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4966)).
- `measure.label` has been accelerated for boolean input images, by using
`scipy.ndimage`'s implementation for this case ([#4945](https://togithub.com/scikit-image/scikit-image/issues/4945)).
- `util.apply_parallel` now works with multichannel data ([#4927](https://togithub.com/scikit-image/scikit-image/issues/4927)).
- `skimage.feature.peak_local_max` supports now any Minkowski distance.
- We now use sparse cross-correlation to accelerate local thresholding
functions ([#4912](https://togithub.com/scikit-image/scikit-image/issues/4912))
- `morphology.convex_hull_image` now uses much less memory by checking hull
inequalities in sequence ([#5020](https://togithub.com/scikit-image/scikit-image/issues/5020))
- Polygon rasterization is more precise and will no longer potentially exclude
input vertices. ([#5029](https://togithub.com/scikit-image/scikit-image/issues/5029))
- Add data optional requirements to allow pip install scikit-image[data]
([#5105](https://togithub.com/scikit-image/scikit-image/issues/5105), [#5111](https://togithub.com/scikit-image/scikit-image/issues/5111))
- OpenMP support in MSVC ([#4924](https://togithub.com/scikit-image/scikit-image/issues/4924), [#5111](https://togithub.com/scikit-image/scikit-image/issues/5111))
- Restandardize handling of Multi-Image files ([#2815](https://togithub.com/scikit-image/scikit-image/issues/2815), [#5132](https://togithub.com/scikit-image/scikit-image/issues/5132))
- Consistent zoom boundary behavior across SciPy versions ([#5131](https://togithub.com/scikit-image/scikit-image/issues/5131), [#5133](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4942))
- The image returned by `data.camera` has changed because of copyright
issues ([#4913](https://togithub.com/scikit-image/scikit-image/issues/4913)).
## Bug fixes
- A bug in `label2rgb` has been fixed when the input image had np.uint8
dtype ([#4661](https://togithub.com/scikit-image/scikit-image/issues/4661))
- Fixed incorrect implementation of `skimage.color.separate_stains` ([#4725](https://togithub.com/scikit-image/scikit-image/issues/4725))
- Many bug fixes have been made in `peak_local_max` ([#2592](https://togithub.com/scikit-image/scikit-image/issues/2592), [#4756](https://togithub.com/scikit-image/scikit-image/issues/4756), [#4760](https://togithub.com/scikit-image/scikit-image/issues/4760),
[#5047](https://togithub.com/scikit-image/scikit-image/issues/5047))
- Fix bug in `random_walker` when input labels have negative values ([#4771](https://togithub.com/scikit-image/scikit-image/issues/4771))
- PSF flipping is now correct for Richardson-Lucy deconvolution work in >2D ([#4823](https://togithub.com/scikit-image/scikit-image/issues/4823))
- Fix equalize_adapthist (CLAHE) for clip value 1.0 ([#4828](https://togithub.com/scikit-image/scikit-image/issues/4828))
- For the RANSAC algorithm, improved the case where all data points are
outliers, which was previously raising an error
([#4844](https://togithub.com/scikit-image/scikit-image/issues/4844))
- An error-causing bug has been corrected for the `bg_color` parameter in
`label2rgb` when its value is a string ([#4840](https://togithub.com/scikit-image/scikit-image/issues/4840))
- A normalization bug was fixed in `metrics.variation_of_information`
([#4875](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4948), [#4972](https://togithub.com/scikit-image/scikit-image/issues/4972))
- A segfault in `draw.polygon` for the case of 0-d input has been fixed
([#4943](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/4886)).
- Fix edge filters not respecting padding mode ([#4907](https://togithub.com/scikit-image/scikit-image/issues/4907))
- Use v{} for version tags with pooch ([#5104](https://togithub.com/scikit-image/scikit-image/issues/5104), [#5110](https://togithub.com/scikit-image/scikit-image/issues/5110))
- Fix compilation error in XCode 12 ([#5107](https://togithub.com/scikit-image/scikit-image/issues/5107), [#5111](https://togithub.com/scikit-image/scikit-image/issues/5111))
## Deprecations
- The `indices` argument in `skimage.feature.peak_local_max` has been
deprecated. Indices will always be returned. ([#4752](https://togithub.com/scikit-image/scikit-image/issues/4752))
- In `skimage.feature.structure_tensor`, an `order` argument has been
introduced which will default to 'rc' starting in version 0.20. ([#4841](https://togithub.com/scikit-image/scikit-image/issues/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 `_ or
`plotly `_. In a similar vein, the `qt` and `skivi`
plugins of `skimage.io` have been deprecated
and will be removed in version 0.20. ([#4941](https://togithub.com/scikit-image/scikit-image/issues/4941), [#4954](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/3327): Add functionality for benchmark coverage ([#3329](https://togithub.com/scikit-image/scikit-image/issues/3329))
- Release process notes have been improved. ([#4228](https://togithub.com/scikit-image/scikit-image/issues/4228))
- `pyproject.toml` has been added to the sdist.
- Build and deploy dev/master documentation using GitHub Actions ([#4852](https://togithub.com/scikit-image/scikit-image/issues/4852))
- Website now deploys itself ([#4870](https://togithub.com/scikit-image/scikit-image/issues/4870))
- build doc on circle ci and link artifact ([#4881](https://togithub.com/scikit-image/scikit-image/issues/4881))
- Benchmarks can now run on older scikit-image commits ([#4891](https://togithub.com/scikit-image/scikit-image/issues/4891))
- Website analytics are tracked using plausible.io and can be visualized on
([#4893](https://togithub.com/scikit-image/scikit-image/issues/4893))
- Artifacts for the documentation build are now found in each pull request
([#4881](https://togithub.com/scikit-image/scikit-image/issues/4881)).
- Documentation source files can now be written in Markdown in addition to
ReST, thanks to `myst` ([#4863](https://togithub.com/scikit-image/scikit-image/issues/4863)).
- update trove classifiers and tests for Python 3.9 + fix pytest config ([#5052](https://togithub.com/scikit-image/scikit-image/issues/5052))
- fix Azure Pipelines, pytest config, and trove classifiers for Python 3.8 ([#5054](https://togithub.com/scikit-image/scikit-image/issues/5054))
- Moved our testing from Travis to GitHub Actions ([#5074](https://togithub.com/scikit-image/scikit-image/issues/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](https://togithub.com/scikit-image/scikit-image/issues/5080))
- Disable Travis-CI builds ([#5099](https://togithub.com/scikit-image/scikit-image/issues/5099), [#5111](https://togithub.com/scikit-image/scikit-image/issues/5111))
- Improvements to CircleCI build: no parallelization and caching) ([#5097](https://togithub.com/scikit-image/scikit-image/issues/5097), [#5119](https://togithub.com/scikit-image/scikit-image/issues/5119))
## Other Pull Requests
- Manage iradon input and output data type ([#4298](https://togithub.com/scikit-image/scikit-image/issues/4298))
- random walker: Display a warning when the probability is outsite [0,1] for a given tol ([#4631](https://togithub.com/scikit-image/scikit-image/issues/4631))
- MAINT: remove unused cython file ([#4633](https://togithub.com/scikit-image/scikit-image/issues/4633))
- Forget legacy data dir ([#4662](https://togithub.com/scikit-image/scikit-image/issues/4662))
- Setup longdesc markdown and switch to 0.18dev ([#4663](https://togithub.com/scikit-image/scikit-image/issues/4663))
- Optional pooch dependency ([#4666](https://togithub.com/scikit-image/scikit-image/issues/4666))
- Adding new default values to functions on doc/examples/segmentation/plot_ncut ([#4676](https://togithub.com/scikit-image/scikit-image/issues/4676))
- Reintroduced convert with a strong deprecation warning ([#4681](https://togithub.com/scikit-image/scikit-image/issues/4681))
- In release notes, better describe skimage's relationship to ecosystem ([#4689](https://togithub.com/scikit-image/scikit-image/issues/4689))
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This PR contains the following updates:
==0.13.1->==0.18.1Release Notes
scikit-image/scikit-image
### [`v0.18.1`](https://togithub.com/scikit-image/scikit-image/releases/v0.18.1) [Compare Source](https://togithub.com/scikit-image/scikit-image/compare/v0.18.0...v0.18.1) # scikit-image 0.18.1 This is a bug fix release and contains the following two bug fixes: - Fix indexing error for labelling in large (>2GB) arrays ([#5143](https://togithub.com/scikit-image/scikit-image/issues/5143), [#5151](https://togithub.com/scikit-image/scikit-image/issues/5151)) - Only use retry_if_failed with recent pooch ([#5148](https://togithub.com/scikit-image/scikit-image/issues/5148)) See below for the new features and API changes in 0.18.0. # 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 standardRenovate configuration
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