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Enregistrement W6912052746 · doi:10.5281/zenodo.15779115

napari: a multi-dimensional image viewer for Python

2025· other· en· W6912052746 sur OpenAlexaff

Notice bibliographique

RevueZenodo (CERN European Organization for Nuclear Research) · 2025
Typeother
Langueen
Domaine
Thématique
Établissements canadiensInnovation Cluster (Canada)
Organismes subventionnairesnon disponible
Mots-clésZoomGridPython (programming language)VisualizationOverlayPixelMode (computer interface)Image (mathematics)

Résumé

récupéré en direct d'OpenAlex

napari 0.6.2 Tue, Jul 01, 2025 We're happy to announce the release of napari 0.6.2! napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for exploring, annotating, and analyzing multi-dimensional images. It's built on Qt (for the GUI), VisPy (for performant GPU-based rendering), and the scientific Python stack (NumPy, SciPy, and friends). For more information, examples, and documentation, please visit our website: https://napari.org/ Highlights The amazing new Grid mode! 🗺️ The visualization of Grid mode has been redone from the ground up! This new Grid mode (#7870) now puts each layer into its own view (a VisPy Viewbox) with cameras linked together. Now, you can pan and zoom one view, and all other views in the grid will follow along. Layers are no longer awkwardly transformed into the same world space and displayed in a grid, only to make comparing the details of each a challenge. Grid based exploration is now fluid, fast, and intuitive, especially when working with large images and 3D+ data! The mouse can even be used over one View, while updating the data, such as a label or shape annotation, in the selected layer of a different view. The usual napari overlays can now also be added to each grid, instead of just the canvas (eg. viewer.scale_bar.gridded = True). Grid mode spacing now works proportionally to the layer extents (i.e. [0,1), as in 0.6.0) or as a pixel value [1,1500) and will automatically adjust if needed. To coincide with this new Grid mode, we have chosen to reverse the ordering of layers in the grid (#8053). The first layer added to the viewer will now be at the top left of the grid, and the last layer added will be at the bottom right; new layers will be added to the bottom right of the grid. If you prefer the previous behavior, you can set the Grid Stride to -1 in the Preferences dialog. The Features Table Widget is now a napari builtin! 📊 The features table from napari-properties-viewer is now a builtin widget in napari (#7877) and greatly improved! This widget allows you to view and edit the properties of Points, Shapes, and Labels layers in a table widget. The widget can be opened from the Layers menu -> Visualize -> Features table widget (napari builtins) or from the command palette. You can also save the properties table to a CSV file. Check out the Features table widget example to learn more. Community developments! 📅 We are excited to share our new active roadmap which is a living document that will be updated as we continue to develop napari. This document is intended to help the community understand the priorities of the napari team and to help us all work together to make napari better. We are also now including all napari related events in the community calendar and as an image.sc post, including conferences, tutorials, sprints, virtual seminars, and more. If you have an event you would like to add, please reach out to us! Some great features for contributors! 🛠️ Contributing documentation is now a much smoother experience! By default, new documentation will build in around 3 minutes, instead of the previous 20 minutes. This speed is thanks to new, slimmer make commands (slimfast by default) that can also be triggered in PRs with a bot (eg. @napari-bot make docs). Read our updated docs contribution guide and reach out for help. The organization of the napari repo has been updated by moving into a src/ directory (#7952). This is modern best practice in Python projects (and what has long been standard in our napari-plugin-template) to avoid issues with relative imports and should now always result in importing the napari version installed in the current environment. For developers, especially of pull requests prior to this release, you may have many merge conflicts to resolve. Please ping the napari team if you would like help resolving these conflicts. There is now public API to access widgets docked in the viewer (#7965). Check out the new documentation on the napari website to learn more about using this API to communicate between widgets. If you previously used viewer.window._dock_widgets, you should now use viewer.window.dock_widgets. New Features Grid mode using vispy ViewBox and linked cameras (#7870) Features table widget as builtin (#7877) Improvements Add check if there is mix of local and non local installation (#7745) Reduce warmup of numba if non numba backend is selected (#7917) Optional rotation handle for selection box overlay + simplify inheritance for Vispy overlays (#7958) Add public API to get access to docked widgets (#7965) Allow to use ViewerModel as annotation of plugin constructor argument (#8002) Update [shapes]: 'make select_all_shapes' keybinding a toggle (#8014) Update[shortcuts]: add Ctrl/Cmd-A as secondary keybinding for select_all_shapes (#8015) Fix Shapes layer to work with Features Table (#8048) Reverse canvas grid order (#8053) Improve tooltips for Grid attributes (#8058) Performance [Shapes] Use the plural methods to update colors of all selected shapes at once (#7995) Bug Fixes Fix scalebar theme connection (#7902) Don't add widgets to non-contributable menus (#7926) Fix handle mouse events (#7936) Fix moving of first/last vertex of polygons added in ring mode (#7942) Update shapes highlight on zoom (#7953) Fix invalidate of extent cache in Layers (#7972) [Points] Fix events.data_indices for ActionType.ADDED event when adding single point (#7983) Fix interaction box initialization (#8011) Fix angles not showing correctly in UI (#8013) Bugfix: ensure multiscale images can be merged using contextual action (#8025) Fix Shapes layer to work with Features Table (#8048) Fix grid stride layering (#8057) Build Tools Bump requests from 2.32.3 to 2.32.4 in /resources (#8010) Documentation Update README to use imshow and add example to generate image (#7989) Update docstring in mouse_drag_callback.py (#8019) Add information about conda version and downloads to badges (#8054) Add links to napari troubleshooting documentation (#8061) Update version switcher for 0.6.1 (docs#713) Update contributing docs page (docs#715) Update code of conduct committee members (docs#716) Add features table widget (docs#718) Update docker build links (docs#720) Add initial documentation about widget communication (docs#721) update grid mode explanation and add video (docs#725) Update installation.md to link to conda getting started not miniconda (docs#726) Update governance docs (docs#729) Initial release notes for alpha of 0.6.2 (docs#734) Add active roadmap document (docs#735) Use darker blue for community meetings in napari calendar (docs#736) Add draft of 0.6.2 release notes (docs#743) 0.6.2rc1 release notes (docs#744) Final 0.6.2 Release Notes (docs#751) Add troubleshooting section about mixed local and non local installations (docs#752) Other Pull Requests Add docs constraints for python 3.12 (#7714) Include Qt PyPI server for pre-releases (#7803) Refactor layer overlays visuals from VispyLayer to VispyCanvas (#7835) Update dask, hypothesis, numpy, tensorstore, vispy (#7948) [pre-commit.ci] pre-commit autoupdate (#7951) Restore image in Readme (#7959) Add cron check to update reader extensions v3 (#7966) Update coverage, dask, fsspec, hypothesis, pydantic, tifffile, vispy (#7967) fix vendored script and trigger workflow on pull_request (#7968) [pre-commit.ci] pre-commit autoupdate (#7970) Remove layers_change event that is marked to be removed in 0.5.0 (#7971) [maintenance] Use Wandalen/wretry.action to auto-retry fail in --pre tests (#7986) Update hypothesis, ipython, jsonschema, tifffile (#7987) [pre-commit.ci] pre-commit autoupdate (#7988) Remove the reset_scroll_progress action and keybinding (#7990) Stop status thread on Keyboard Interruption (Ctrl+C) (#7994) Update hypothesis, magicgui, pandas, pyqt6, pytest, pytest-pretty (#8000) Update pyproject.toml to fix coverage paths (alt) (#8001) [Maintenance] Remove redundant initialization in Points layer and restructure for clarity (#8005) Fix numba fail of compile on GHA macOS runners (#8018) Update certifi, coverage, hypothesis, pydantic, superqt, tifffile, xarray (#8029) Update hypothesis, pytest, superqt (#8036) Stop benchmark reporting if benchmark action is skipped (#8037) Update app-model pin to >=0.4.0, update hypothesis, pygments, scipy (#8041) [pre-commit.ci] pre-commit autoupdate (#8042) Bump bermuda to 0.1.5 (#8052) Update hypothesis, lxml, numpydoc (#8060) Fix comment and manual dispatch triggered build jobs (docs#723) Test passing PR number instead of ref on triggered build (docs#738) [maint] fix circleCI branch naming in trigger action (docs#739) [Enh] When ready-to-merge is applied, do a full build of docs (docs#745) Only build artifact on ready-to-merge label (docs#749) 13 authors added to this release (alphabetical) (+) denotes first-time contributors 🥳 Ashley Anderson - @aganders3 Carol Willing - @willingc Draga Doncila Pop (docs) - @DragaDoncila Grzegorz Bokota (docs) - @Czaki Jacopo Abramo - @jacopoabramo + Juan Nunez-Iglesias (docs) - @jni Lorenzo Gaifas (docs) - @brisvag Lukasz Migas - @lukasz-migas Maximilian Mayrhauser - @Llewi + Melissa Weber Mendonça - @melissawm Peter Sobolewski (docs) - @psobolewskiPhD Rahul Kumar - @rahul713rk + Tim Monko (docs) - @TimMonko 11 reviewers added to this release (alphabetical) (+) denotes first-time contributors 🥳 Ashley Anderson - @aganders3 Carol Willing - @willingc Draga Doncila Pop (docs) - @DragaDoncila Grzegorz Bokota (docs) - @Czaki Jacopo Abramo - @jacopoabramo + Juan Nunez-Iglesias (docs) - @jni Lorenzo Gaifas (docs) - @brisvag Melissa Weber Mendonça - @melissawm Peter Sobolewski (docs) - @psobolewskiPhD Tim Monko (docs) - @TimMonko Wouter-Michiel Vierdag - @melonora

Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.

Comment cette classification a été obtenuedéplier

Prédiction machine sur la base complète

Imitation des enseignants

Ni prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.

score de la tête « metaresearch » (Codex)0,002
score de la tête « metaresearch » (Gemma)0,005
Version: metacan-v3-hybrid-931329e0061cStatut de validation: machine_predicted_unvalidated
Catégories candidatesCharge utile insuffisante (le modèle a refusé de juger)
Catégories consensuellesaucune
DomaineSignal candidat: aucune · Signal consensuel: aucune
Devis d'étudeSignal candidat: Sans objet · Signal consensuel: Sans objet
GenreSignal candidat: Logiciel · Signal consensuel: Logiciel
Score de désaccord entre enseignants0,321
Score d'incertitude au seuil0,969

Scores du classifieur distillé par catégorie (deux têtes)

CatégorieCodexGemma
Métarecherche0,0020,005
Méta-épidémiologie (sens strict)0,0020,002
Méta-épidémiologie (sens large)0,0010,002
Bibliométrie0,0020,001
Études des sciences et des technologies0,0010,001
Communication savante0,0040,006
Science ouverte0,0050,005
Intégrité de la recherche0,0020,004
Charge utile insuffisante (le modèle a refusé de juger)0,3210,297

Scores machine (provisoires)

Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.

Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.

Tête enseignante Opus0,036
Tête enseignante GPT0,280
Écart entre enseignants0,244 · la distance entre les deux têtes enseignantes sur ce seul travail
Statut de validationscore_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découle

Classification

machine, non validée

Prédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.

Devis d'étudeSans objet
Domainenon disponible
GenreLogiciel

Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».

En bref

Citations6
Publié2025
Routes d'admission1
Résumé présentoui

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