Published July 25, 2024 | Version v0.5.1
Software Open

napari: a multi-dimensional image viewer for Python

Creators

  • 1. Chan Zuckerberg Initiative
  • 2. Harvard Medical School
  • 3. University of Warsaw, Faculty of Mathematics, Informatics, and Mechanics
  • 4. Monash eResearch Centre, Monash University
  • 5. The Jackson Laboratory
  • 6. Gutsche Lab - University of Grenoble
  • 7. MRC-LMB
  • 8. Monash University
  • 9. Iber Lab - ETH ZĂŒrich
  • 10. Quansight
  • 11. European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
  • 12. Chan Zuckerberg Biohub
  • 13. Harvard Medical School, BIDMC
  • 14. SETI Institute/NASA ARC
  • 15. Quansight Labs
  • 16. Laboratory for Optics and Biosciences, Ecole Polytechnique, INSERM, CNRS, Palaiseau, France
  • 17. Friedrich Miescher Institute for Biomedical Research (FMI), Basel (Switzerland)
  • 18. EMBL Heidelberg, Germany
  • 19. University of California, Irvine
  • 20. Tel Aviv University, Israel
  • 21. Ramona Optics Inc, Durham, North Carolina, USA
  • 22. University College London
  • 23. Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
  • 24. UniversitĂ€tsmedizin Greifswald
  • 25. Chan Zuckerberg Initiative Foundation
  • 26. UCL & The Alan Turing Institute
  • 27. EMBL Heidelberg
  • 28. MetaCell
  • 29. Delft University of Technology
  • 30. Apex Systems
  • 31. University of California, Los Angeles
  • 32. Georg-August-UniversitĂ€t Göttingen
  • 33. University Hospital WĂŒrzburg - Institute of Neuroradiology
  • 34. Algarve Centre of Marine Sciences (CCMAR)
  • 35. Yikes LLC
  • 36. Brown University
  • 37. NanoString Technologies, Inc.
  • 38. European Bioinformatics Institute - European Molecular Biology Laboratory
  • 39. University of Wisconsin-Madison
  • 40. AI lab for Living Technologies, University Medical Centre Utrecht (The Netherlands)
  • 41. DFG cluster of excellence 'Physics of Life', TU Dresden
  • 42. Aix Marseille University, CNRS, Fresnel, I2M, IBDM, Turing Centre for Living systems
  • 43. TU-Dresden / EPFL
  • 44. ETH Zurich / University of Zurich
  • 45. Tobeva Software

Description

napari 0.5.1

Thursday, Jul 25, 2024

We're happy to announce the release of napari 0.5.1!

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

napari 0.5.1 is a bugfix release hot on the heels of napari 0.5.0. It fixes a critical bug with creating viewers multiple times within a single IPython/Jupyter session (#7106), as well as regressions with viewing multiscale 3D time series (#7103) and with converting image layers to labels layers (#7095).

It also fixes a bug with NumPy 2 support (#7104) and our storing of layer axis info when using the channel_axis keyword argument for images (#7089).

Read on for the full list of changes since the last version from just two weeks ago!

Improvements

  • [enh] add an add_plane convenience method to ClippingPlaneList (#6921)
  • Cleanup _image_key_bindings (#7116)
  • Add napari-plugin-manager to optional info list (#7117)

Bug Fixes

  • Move the _is_created assignment to the top (#5078)
  • [Bugfix] Fix logic in setting settings using env vars. (#6669)
  • Fix handling of units and axis_labels in add_image (#7089)
  • Fix label conversion with proj mode (#7095)
  • Account for displayed dimensions in multiscale translate adjustment (#7103)
  • fix call of np.clip in _update_thumbnail (#7104)
  • Always add Empty context key, even if action is already registered (#7106)
  • fix condition of adding asterix, when save reader of path (#7112)
  • Normalize path when searching for a plugin to open file (#7127)

Documentation

  • Add link to partners in README.md (#7069)
  • Restore README image (#7098)
  • Update docs constraints files for new napari-sphinx-theme release (#7111)
  • Update release notes for 0.5.1 with new PRs (docs#466)
  • Update Bundled App Installation Instructions (docs#74)
  • Update Makefile to be consistent (docs#448)
  • Use plausible configuration by the PyData Sphinx Theme (docs#453)
  • More fixes to contributing documentation guide (docs#454)
  • Add location field to community calendar (docs#455)
  • Fix footer items (docs#456)
  • Add docs about the new napari-base structure (docs#457)
  • Add draft 0.5.1 release notes (docs#464)
  • Update draft warning on 0.5.1 release notes (docs#465)
  • Update release notes for 0.5.1 with new PRs (docs#466)

Other Pull Requests

  • Remove ready to merge on update of constraints PR (#6984)
  • Update app-model, coverage, dask, fsspec, hypothesis, imageio, ipython, jsonschema, matplotlib, napari-svg, numpy, pillow, pint, pydantic, pyqt5, pyqt6, pytest, scipy, tifffile (#7045)
  • Add actionlint on CI (#7049)
  • fix: set target_commitish for commit sha to fix benchmarks (#7091)
  • Use viewer.layers instead of _layers.model().sourceModel()._root for dummy context creation (#7109)
  • Limit setuptools vesion for minimum requirements test (#7110)
  • [Maint] Update dockerfile for xpra source change (#7115)
  • Fix pinning packages workflow by remove special pinning from macOS and add special for Windows (#7119)
  • Trigger docs deployment on tagged commit (#7122)
  • Update version switcher to include 0.5.0 (docs#452)
  • deploy docs on manual trigger (docs#462)
  • Add actionlint to prevent GHA workflow errors (docs#463)

9 authors added to this release (alphabetical)

(+) denotes first-time contributors đŸ„ł

11 reviewers added to this release (alphabetical)

(+) denotes first-time contributors đŸ„ł

Notes

If you use this software, please cite it using these metadata.

Files

napari/napari-v0.5.1.zip

Files (3.4 MB)

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md5:36af2731e07d737ce15acc35ce903744
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Additional details

Related works

Is supplement to
Software: https://github.com/napari/napari/tree/v0.5.1 (URL)