napari 0.4.17

We’re happy to announce the release of napari 0.4.17! napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing large multi-dimensional images. It’s built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy).

For more information, examples, and documentation, please visit our website: https://github.com/napari/napari

Highlights

This release is focused on documentation improvements and bug fixes, with few changes to napari’s API. We picked out a few highlights, but keep reading below for the full list of changes!

Minimum blending and inverted colormaps

We added a new blending mode, minimum, in #4875, along with some inverted colormaps by @cleterrier. The new mode and colormaps enable visualizing data as color intensities on a white background. This is particularly nice when using the Light theme. For more inspiration see #invertedLUT on Twitter and the built-in napari example examples/minimum_blending.py.

Option to edit second shortcut in preferences

We improved customization of napari preferences by allowing you to define a second, alternative shortcut for each napari action. This allows you, for example, to have both numeric (e.g. 1, 2, 3 - related to button positions) and semantic (F - for fill) shortcuts defined for use in napari.

One line image loading

We added napari.imshow in #4928 as a convenience function to load image data and return both a Viewer and the image Layer all in one line.

viewer, layer = napari.imshow(data)

See the docstring of napari.imshow for more details.

Experimental support for Qt6

We added some basic support for PyQt6 and PySide6 in #3707, though we expect some issues. If you need or want to use Qt6, please try this out and report any bugs you find. If you plan to use PySide6 specifically, please use Python 3.10 to avoid issues with older versions of Python.

Multi-color text

We added support for assigning multiple colors for text annotations of points and shapes in #4464. See examples/add_points_with_multicolor_text.py This uses the API that we intend to spread elsewhere for other style attributes like Points.face_color, so if you are a heavy user of those types of attributes you should try this out and leave feedback on Zulip or create issues on GitHub.

New Features

  • Multi-color text with color encodings (#4464)

  • add layer reader in tooltip and info dialog (#4664)

  • Feature: Minimum blending (#4875)

  • Add option for forcing plugin choice when opening files in the GUI (#4882)

  • Add saving folders to preferences (#4902)

  • Add napari.imshow to return viewer and layers (#4928)

  • Option to load all dock widgets (#4954)

  • Feature: register a keyboard shortcut for preserve_labels checkbox (#5017)

  • Add option to edit second shortcut in settings (#5018)

  • Autorepeatable keybindings & keybindings for label brush size (#5086)

Improvements

  • support PyQt6, remove logic for compile_qt_svgs (#3707)

  • Improvements on scale bar (#4511)

  • allow use of validate_all=True on nested evented models (#4551)

  • Add modal dialogs for window/application closure (#4637)

  • Optimization: convert point slice indices to floats (#4648)

  • honor confirm close settings when quitting (#4700)

  • Use custom color field classes in all models (#4704)

  • napari.viewer.current_viewer fallback ancestor (#4715)

  • Add public API for dims transpose (#4727)

  • Add a public API for the setGeometry method of _qt_window (#4729)

  • Expose points layer antialiasing control publicly (#4735)

  • Use npe2 list to show plugin info (#4739)

  • Allow pandas.Series as properties values (#4755)

  • Allow stack to be specified multiple times (#4783)

  • Refactor: use app-model and in-n-out (#4784)

  • Fix point experimental_canvas_size_limits and set sane defaults (#4790)

  • Improve “select all” logic in points layer, adding “select all across slices” behavior (#4809)

  • Make docked widgets of qt_viewer lazy (#4811)

  • Restore Labels, Points and Shapes layer mode after hold key (#4814)

  • Confirmation on close, alternative approach (#4820)

  • add path specificity scoring (#4830)

  • [Automatic] Update albertosottile/darkdetect vendored module (#4845)

  • Add plugin reader warning dialog (#4852)

  • Fix python name in macOS menu bar (#4989)

  • Explicit convert color to string when compile resources (#4997)

  • Add link to docs artifact to pull requests (#5014)

  • Reverse order of plugin name and widget name (#5054)

Performance

  • Optimization: convert vector slice indices to floats (#4794)

Bug Fixes

  • Fix: Always save settings after migration (#4490)

  • Make sure reader dialog pops open if File -> Open Sample is compatible with multiple readers (#4500)

  • Do not add duplicate layers (#4544)

  • Disconnect a removed slider’s _pull_label callback from the axis label change event (#4557)

  • Clean status message after leave canvas (#4607)

  • Alternate fix for alt-text issues (#4617)

  • Fix numpy version comparison for dev versions of numpy (#4622)

  • Restore “show all key bindings” shortcut (#4628)

  • Raise error when rgb True but data not correct dims (#4630)

  • Define different shortcuts for different screenshot actions in file menu (#4636)

  • Do not use keyword argument for QListWidgetItem parent set in constructor (#4661)

  • fix: fix manifest reader extensions, ensure that all builtins go through npe2 (#4668)

  • Fix source of copied layer events by use layer.as_layer_data_tuple (#4681)

  • Tracks tail update fix beyond _max_length (#4688)

  • Keep order of layers when select to save multiple selected layers (#4689)

  • Apply shown mask to points._view_size_scale (#4699)

  • Color edit without tooltip fix (#4717)

  • fix presentation and enablement of npe1 plugins (#4721)

  • fix clim init for dask arrays (#4724)

  • split Image interpolation on two properties, interpoltion2d and interpolation3d (#4725)

  • Fix bug in deepcopy of utils.context.Expr (#4730)

  • Fix _get_state for empty Vectors and Points layers (#4748)

  • Stop slider animation on display and dimension changes (#4761)

  • Fix deepcopy for trans objects when passing args (#4786)

  • Make newly added points editable (#4829)

  • Allow empty tuple layer to be returned #4571 (#4831)

  • Disable notifications if no main window (#4839)

  • Fix multiscale level selection when zoomed out (#4842)

  • Move vector mesh generation to napari vispy visual and fix vectors refesh (#4846)

  • Fix creation QtViewer for ViewerModel with already added layers (#4854)

  • Update hub.py (#4863)

  • Fix viewer.reset() throws TypeError (#4868)

  • fix icon urls for close dialog (#4887)

  • Fix missing slice from dims (#4889)

  • Raise exception when layer created with a scale value of 0 (#4906)

  • Fix for display of label colors (#4935)

  • Initialize plugins before validating widget in napari -w {plugin} (#4948)

  • Fix resize window problem by to long text in help (#4981)

  • Fix throttled status updates by ensuring GUI updates occur on the main thread (#4983)

  • Fix throttled status updates by use QSignalThrottler in _QtMainWindow constructor (#4985)

  • Ensure non-negative edge width (#5035)

  • Fix the wrong guardian for the build tooltip when bind button (#5075)

  • disable mip and minip cutoffs if opaque blending (#5085)

  • Fix blending presets. (#5087)

  • Bugfix: disable opacity slider for opaque blending (#5088)

  • Add extra garbage collection for some viewer tests (#5108)

  • Fix typestub and check manifest problems with build package (#5112)

  • Fix error with “None” key press (#5115)

  • Fix shortcuts deleting (#5119)

  • Standardise file extension when reading (#5121)

  • Fix slow points (#5133)

  • Use cross shape when cursor is small (#5141)

  • Fix exception when rendering colorbar from a label_colormap (#5154)

  • Make imshow defaults the same as add_image (#5156)

  • Remove uninstalled plugin from plugin manager (#5190)

  • In Volume shader for iso surface ommit point that color has alpha equal to 0 (#5227)

  • Move theme files to cache dir (#5248)

  • Fix screenshot size argument (#5251)

API Changes

  • Removed unused private Layer._position (#4604)

  • Add public API for dims transpose (#4727)

  • Add a public API for the setGeometry method of _qt_window (#4729)

  • Expose points layer antialiasing control publicly (#4735)

Deprecations

  • Deprecate layers.move_selected (#4559)

  • Update deprecation warnings with versions (#4757)

  • Make viewer.events.layers_change event deprecated (#4895)

  • Deprecate moved IO utilities (#5284)

Build Tools

  • [pre-commit.ci] pre-commit autoupdate (#4506)

  • Limit workflows runs based on file changes (#4555)

  • [Automatic] Update albertosottile/darkdetect vendored module (#4561)

  • Dockerfile: stay on 20.04/LTS for python3.8 (#4572)

  • Block lxml 4.9.0 version (#4616)

  • Remove meshzoo from napari (#4620)

  • ci(dependabot): bump peter-evans/create-pull-request from 3 to 4 (#4675)

  • ci(dependabot): bump docker/build-push-action from 2.5.0 to 3 (#4676)

  • ci(dependabot): bump actions/setup-python from 3 to 4 (#4677)

  • ci(dependabot): bump toshimaru/auto-author-assign from 1.3.4 to 1.5.0 (#4678)

  • ci(dependabot): bump docker/metadata-action from 3 to 4 (#4679)

  • ci(dependabot): bump styfle/cancel-workflow-action from 0.9.1 to 0.10.0 (#4770)

  • ci(dependabot): bump actions/download-artifact from 2 to 3 (#4771)

  • ci(dependabot): bump actions/github-script from 5 to 6 (#4772)

  • ci(dependabot): bump bruceadams/get-release from 1.2.2 to 1.2.3 (#4773)

  • ci(dependabot): bump docker/login-action from 1.9.0 to 2 (#4774)

  • Bump vispy 0.11.0 (#4778)

  • [pre-commit.ci] pre-commit autoupdate (#4779)

  • ci(dependabot): bump toshimaru/auto-author-assign from 1.5.0 to 1.6.1 (#4890)

  • Docker: Update xpra’s apt too (#4901)

  • Remove leading b from briefcase macOS support build numbers (#5152)

  • Block imageio 2.22.1 release in setup.cfg (#5168)

  • Remove osx-arm64 from conda bundle (#5255)

Documentation

  • Proposal to accept NAP-1 - add institutional and funding partners to governance (#4458)

  • Fix ImportErrors for instance attributes when building docs (#4471)

  • Update viewer tutorial (#4473)

  • Fix selection events documentation for LayerList (#4478)

  • add ABRF LMRG workshop recording (#4487)

  • Add alt_text (#4502)

  • DOC: misc syntax updates and typoes (#4517)

  • Start a NAP about conda packaging for napari (#4519)

  • Add CZI as an Institutional and Funding Partner (#4524)

  • add I2K workshop (#4528)

  • Add NAP1 to ToC. (#4552)

  • Forward port of release note updates for 0.4.16rc2 and rc3 (#4563)

  • Add option to use npe2 shim/adaptor for npe1 plugins (#4564)

  • Forward port further 0.4.16 release note changes (#4592)

  • Discuss the approval of NAP-2 (conda-based packaging for napari) (#4602)

  • Add versioned API docs workflow (#4635)

  • Update installation instruction in documentation (#4639)

  • Fix docs for shape/points layer properties (#4659)

  • Embeding viewers in plugins widget example (#4665)

  • Add NAP-3: Spaces (#4684)

  • Fix NAP-1 status/type (#4685)

  • Add new core devs to docs (#4691)

  • add ‘napari-xpra’ target to dockerfile (#4703)

  • Fix Image parameter docs (#4750)

  • Make references to examples link there (#4767)

  • Add documentation about apply napari style to separate windows (#4780)

  • Fix documentation link errors. (#4787)

  • Fixing readme typo (#4791)

  • Add Talley to the steering council (#4798)

  • Update documenation : install plugin from URL (#4799)

  • Accept NAP-2: Distributing napari with conda-based packaging (#4810)

  • Fixes duplicate label warnings in the documentation (#4823)

  • added description of how to save layers without compression (#4832)

  • Add the ability to return a List[Layer] in magicgui (#4851)

  • Fix NAP-3 table of contents (#4872)

  • Feature: Minimum blending (#4875)

  • NAP 4: asynchronous slicing (#4892)

  • Correct minor typo in quick_start.md (#4908)

  • Add Google Calendar ID to directive (#4914)

  • Fix docs dependencies (#4915)

  • Maintenance: Add title to example and remove unused redirect configuration (#4921)

  • Use napari/packaging for Conda CI (#4923)

  • Correct minor typos on ‘Contributing resources’ page (#4927)

  • DOC Add docs on napari models and events (#4929)

  • DOC Fix add image examples (#4932)

  • add SciPy 2022 materials (#4934)

  • Remove repeated items in gallery ToC. (#4936)

  • DOC Remove references to old add_volume (#4939)

  • Fix calendar ID (#4944)

  • DOC Add docs on how to run napari headless (#4955)

  • Removes deprecated configuration options for notebooks from docs build (#4958)

  • Update async slicing discussion section with PR feedback (#4959)

  • DOC Add section on downloading CI built docs (#4961)

  • DOC Expand explanation of interaction_box_image example (#4962)

  • DOC: Fix some incorrect parameters names. (#4965)

  • DOC Add headless doc to toc (#4970)

  • Remove preliminary admonition for last two release notes (#4974)

  • Enabe tags in gallery examples. (#4975)

  • Update viewer screenshot in docs and make more prominent on napari.org (#4988)

  • Move the docs downloading screenshots to LFS (#4990)

  • DOC Enable intersphinx linking in examples (#4992)

  • Fix broken links in Napari Code of Conduct (#5005)

  • Add linkcheck (#5008)

  • Add link to docs artifact to pull requests (#5014)

  • Add release notes for 0.4.17 (#5031)

  • add #4954 to release notes (#5038)

  • add new PRs merged for 0.4.17 to release notes (#5045)

  • Proposal to accept NAP #4: asynchronous slicing (#5052)

  • Update v0.4.17.rc0 release notes (#5058)

  • update core dev group to remove Ziyang and Justine (#5059)

  • Better script for prepare release notes (#5061)

  • Bugfix: disable opacity slider for opaque blending (#5088)

  • Update links in NAP-2 (#5099)

  • Update release notes for v0.4.17rc1 (#5110)

  • Update release notes for v0.4.17rc3 (#5147)

  • Add Peter Sobolewski (@psobolewskiPhD) to list of Core Developers (#5189)

  • Update release notes for v0.4.17rc5 (#5268)

  • Update release notes for v0.4.17rc6 (#5280)

  • Update release notes for v0.4.17rc7 (#5295)

Other Pull Requests

  • Fire features event on Labels feature change (#4481)

  • Image layer control dtype normalization for tensorstore compatibility (#4482)

  • Reorder tests (#4483)

  • Test if events for all properties are defined (#4486)

  • throttle status update (#4488)

  • use inject_napari_dependencies in layer_actions commands (#4489)

  • Add _get_value_3d to surface (#4492)

  • Reduce canvas margin (#4496)

  • Fix trailing comma fixes black formatting (#4498)

  • Update layer list context keys (#4499)

  • Do not allow None when coercing encodings (#4504)

  • [Automatic] Update albertosottile/darkdetect vendored module (#4508)

  • Try to upload pytest json report as artifact. (#4518)

  • Try to speedup tests. (#4521)

  • change default blending mode on image layer to translucent no depth (#4523)

  • Accessor refactor (#4533)

  • Add explanation what EmitterGroup.block_all and EmitterGroup.unblock_all do in docstring (#4536)

  • Revert “change default blending mode on image layer to translucent no depth” (#4540)

  • add ci for asv benchmark suite (#4554)

  • Fixes/modifications to nested list model and Group in prep for layergroups (#4560)

  • Fix macos release version comparison in main (#4565)

  • Update base docker image to ubuntu 22.04, optimize container size. (#4568)

  • Patch scikit-image cells3d data function when testing examples (#4578)

  • Add question about qt backends to PR tests (#4583)

  • Don’t build bundle in PRs on doc changes (#4584)

  • Fix Auto-open trans issue. (#4586)

  • Internationalisation testing. (#4588)

  • Add test for QtPerformance widget (#4591)

  • Split coverage on parts (#4595)

  • More updates to the ignored translations file and translation CI infrastructure (#4596)

  • feat: add codespace (#4599)

  • Enable patch coverage reporting (#4632)

  • Add tests for qt_progress_bar.py (#4634)

  • Remove some sleepy tests, wait with timeout instead (#4638)

  • Speed up notebook display tests (#4641)

  • build: slight updates/de-dups in setupcfg (#4645)

  • test: Speed up test_viewer tests, split out pyqt5/pyside2 tests again (#4646)

  • Move test examples on end of test run them in different CI job (#4647)

  • Allow to trigger test_translation manually (#4652)

  • Limit comprehensive test concurrency to 1. (#4655)

  • Do not run asv on push (#4656)

  • ci: fix tox factor names in tests (#4660)

  • test: speed up magicgui forward ref tests (#4662)

  • Remove unused points _color state (#4666)

  • test: Cleanup usage of npe2 plugin manager in tests (#4669)

  • add dependabot for github actions dependencies (#4671)

  • Use cache: pip from actions setup-python (#4672)

  • Remove restore_settings_on_exit test util (#4673)

  • bump npe2 version, use new features (#4686)

  • [pre-commit.ci] pre-commit autoupdate (#4687)

  • Remove unnecessary uses of make_napari_viewer (replace with ViewerModel) (#4690)

  • Design issue template assignees (#4701)

  • Refactor label painting by moving code from mouse bindings onto layer, adding staged history and paint event (#4702)

  • Split out builtins into another top-level module (#4706)

  • use python 3.9 for mac tests until numcodecs 3.10 wheels are available (#4707)

  • Remove print statement in settings (#4718)

  • Use some features from npe2 v0.5.0 (#4719)

  • use same coverage report like in pull requests (#4722)

  • Update translation documentation link in pull request template (#4728)

  • Cleanup list of non-translatable strings. (#4732)

  • Add mini interactive prompt to edit string_list.json (#4733)

  • Do not inform about coverage untill all CI jobs are done (#4751)

  • Refactor NapariQtNotification test for better cleaning Qt objects (#4763)

  • Set focus on QtViewer object after creating main window (#4768)

  • Add missed call of running_as_bundled_app in __main__ (#4777)

  • test: fix ability to use posargs with tox (#4788)

  • Allow dunder methods use in PublicOnlyProxy (#4792)

  • add update_mesh method (#4793)

  • mock npe1 plugin manager during tests (fix tests with npe1 plugins installed) (#4806)

  • [Automatic] Update albertosottile/darkdetect vendored module (#4808)

  • Improve using Qt flags by direct use enums. (#4817)

  • Move searching parent outside NapariQtNotification constructor (#4841)

  • Enable plugin menu contributions with app-model (#4847)

  • Raise better errors from lazy getattr (#4848)

  • Allow to undock docked viewers in multiple viewers example (#4859)

  • MAINT: disable failing conda bundling. (#4878)

  • MAINT: Work around conda bundling issue. (#4883)

  • remove a few more qtbot.wait calls in tests (#4888)

  • use npe2api in plugin install dialog (#4893)

  • Add perfmon directory for shared configs and tools (#4898)

  • Conda: fix MacOS signing (#4904)

  • Improve error message for a failed write (#4913)

  • Minor type fix (add Optional) (#4916)

  • add user keymap (#4946)

  • MAINT: temporary mypy disabling as it’s failing everywhere. (#4950)

  • Adjust the slider value to include current_size (#4951)

  • MAINT: re-enable type checking workflow (#4960)

  • MAINT: bump napari-console to 0.0.6. (#4967)

  • [pre-commit.ci] pre-commit autoupdate (#4968)

  • Fix: bump app-model, add test for layer buttons (#4972)

  • Add FUNDING.yml file to enable sponsor button and increase discoverability of option to sponsor napari (#4978)

  • Start adding a CODEOWNERS file. (#4993)

  • Add emacs temporary & local files to .gitignore (#4998)

  • Set fixpoint before move for shapes (#4999)

  • Fix sys.path issue with subprocess relaunch in macOS (#5007)

  • MAINT: update issue failing template (#5012)

  • [pre-commit.ci] pre-commit autoupdate (#5015)

  • Fix shift selection for points (#5022)

  • Revert “Fix sys.path issue with subprocess relaunch in macOS” (#5027)

  • Use Source object to track if a layer is duplicated (#5028)

  • Revert “Revert “Fix sys.path issue with subprocess relaunch in macOS”” (#5029)

  • update some of the ignored translations (#5032)

  • MAINT: fix a couple of trans._. (#5034)

  • MAINT: Update Future Warning. (#5037)

  • MAINT: Unnecessary formatting of constant. (#5044)

  • Small shortcuts preference pane wording update after #5018 (#5049)

  • Small changes to points defaults. (#5050)

  • MAINT: Don’t deprecate something that was never stable. (#5068)

  • Try to avoid latest shiboken that break CI (#5073)

  • Add new core libraries to napari info (#5077)

  • Update config directory paths for perfmon tools (#5081)

  • Update some strings to be translated, some to be ignored (#5082)

  • Workaround for PySide6 problem (#5244)

  • Revert raising of PySide6 version error (#5272)

  • Remove obsolete example code (#5274)

48 authors added to this release (alphabetical)

32 reviewers added to this release (alphabetical)

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