napari: a multi-dimensional image viewer for Python

napari 0.6.0 Fri, Apr 11, 2025 🚧 These notes are under construction while in pre-release 🚧 We're happy to announce the release of napari 0.6.0! The right-handed release! This release features major changes so read on to see how they might affect you! 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 Summary Updated viewer handedness ✋ Command palette 🎨 Display polygons with holes Transition to npe2 plugin engine by default Many other GUI improvements Updated viewer handedness ✋ So. Funny story. 😅 For (checks notes) 5 years or so, napari has had a 3D view, and for those 5 years, for almost all datasets, that view has been a mirror image of the 3D object they were trying to represent. Any biologists among you might have noticed that loading 3D molecular coordinates of DNA would result in a left-handed helix, while anatomists among you might have been surprised by how many of your samples suffered from situs inversus totalis! By and large, many things that people care about work exactly the same in the mirror world — volume measurements, forces, tracking, speed, ... — so this bug has gone mostly unnoticed, or noticed and shrugged off and unfixed for all this time. But it's important for some things! Your heart is on the left side of your body, but the right side of your mirror image's. This can be critical, for example, when using software to plan surgery! Thankfully, we are not aware of any cases of napari being used in this way. 😅 napari uses zyx coordinates instead of xyz because it is the most natural way to work with NumPy arrays and the rest of the scientific Python imaging ecosystem. Flipping the axes in this way also changes the handedness of the space, unless you also flip the direction of one of the dimensions. The simplest way to illustrate this is this 3D model of a right shoe, which looks like this in previous versions of napari: and in 0.5.6+, thanks to #7488: Most users won't notice. But if you were among the users that noticed and you implemented workarounds in your code (such as setting the z-scale to a negative number), now is a good time to undo the workarounds for newer versions of napari! If you run into any issues please get in touch on GitHub issues or on our Zulip chat room! On the user space, we now offer several options to orient the axes any way you like: Through the camera API: the Viewer.camera instance gains two new attributes: orientation, and orientation2d, which is just the last two dimensions of orientation. You can set the direction that the depth, vertical, and horizontal axes point to, respectively in that order, as follows (#7663): # 2D viewer.camera.orientation2d = ('up', 'right') # 3D viewer.camera.orientation = ('away', 'up', 'right') See an example of this in action in {ref}sphx_glr_gallery_xarray-latlon-timeseries.py. Through the UI: By right clicking on the dimension toggle in the viewer, and setting the axis orientations using the drop-down menus (#7686), which in 3D will further indicate whether the resulting coordinate frame is right-handed or left-handed (#7770): Through the startup settings: If you want to use a specific axis orientation consistently, you can set the default orientation on startup by changing the relevant settings (#7787: To restore the orientation from napari 0.5.6 and earlier, change the Depth axis setting to "away" (i.e. depth axis points away from you). Command palette 🎨 Tired of mousing around? Thanks to #5483, napari gains a command palette! Press {kbd}Ctrl/Command+Shift+P and start typing the name of the action you want to use, and press {kbd}Enter when you've highlighted it. It even works with plugins! This is the culmination of many months of work porting napari's actions to Talley Lambert's app-model. 🥳 (video of command palette) There's still lots of work to be done here, but in the meantime, give it a try! We on the team have found it very hard to go back to using napari without the palette! Feature improvements to Shapes layers ⚠️ In 0.6.0a1 and earlier, this only works when installing PartSegCore-compiled-backend and toggling the "use compiled triangulation" option in the advanced preferences. In 0.6.0 it will work with all triangulation backends. ⚠️ Finally, napari Shapes layers can now display polygons with holes in them, which starts to open it up for use with mapping data, among other things! (#7566, #6654]) Implementing this feature also eliminated a lot of bugs in our polygon drawing code, which could cause crashes. If you've had issues with Shapes layers before, now might be a good time to give them another try! Transition to npe2 plugin engine npe2 was introduced over four years ago, with napari 0.4.12. npe2 has paved the way for new plugin functionality, such as adding menu items and the command palette. We are now beginning the process of deprecating npe1 (napari-plugin-engine) plugins, which we need to do to continue to improve npe2 functionality, for example in file readers, which is currently very entangled with npe1 code. To aid this migration, npe1 plugins will now be automatically converted to npe2 by default. This may break some features if the plugins relied on import-time behavior. (#7627) During the 0.6.x series, if some plugin functionality is broken by the automatic conversion, you can turn off this conversion in the plugin preferences. However, the option to not convert npe1 plugins will be removed in 0.7.0, and npe1 plugins will only work through automatic conversion. We anticipate 0.7.0 will be released in the second half of 2025. If you encounter conversion issues in a plugin you rely on, please contact the plugin authors to encourage them to migrate their plugin to the npe2 system. For more details on this change and how it affects plugins, see the detailed guide. If you are a plugin author and your plugin is not yet npe2-compatible, please see our npe2 migration guide, and, if you encounter any issues, get in touch in our Plugins Zulip chat channel or by coming to one of our community meetings. GUI improvements You'll notice the main napari GUI is subtly (or not so subtly) different in 0.6.0. Here are some of the improvements: Buttons now have an indicator to show whether they contain an extra menu when right-clicking. (#7556) The button to change between 2D and 3D views much more clearly shows what it does. (#7608) … And it has an extra menu with lots of options to control the camera! (#7626) You can now add a bit of spacing between layers in grid mode (and control it in the grid mode right-click menu!) (#7597) The colormap indicator in image layers is now a button, allowing you to create a linear colormap with any color! (#7600) If you select multiple layers in the layer list, you can now see the status display of all the selected layers in the status bar (#7673) Other stuff For developers: napari now depends on Python 3.10+ and Pydantic v2.2. We've supported both pydantic 1 and 2 since 0.4.19, but we're now ready to take advantage of performance and API improvements in Pydantic 2. If your library depends on Pydantic 1.x, now would be a good time to upgrade, or it will not be compatible with napari going forward. (#7589) Flip z axis on 3D camera to default to right-handed frame (#7488 redux) (#7554) Update configuration to drop python 3.9 and add python 3.13 (#7603) Change deprecation to 0.7.0 for private attribute access from PublicOnlyProxy (#7730) Maintain 3D camera angles when switching between 2D and 3D views (#7765) New Features Implement command palette widget (#5483) Add Grid Mode Spacing to change distance between layers (#7597) Enable creation of custom linear colormaps in layer controls (#7600) Add API to Camera model to flip axes (#7663) Show layer status for all visible layers (#7673) Expose new camera orientation API in GUI in ndisplay popup widget (#7686) Improvements Add numba warmup step when creating empty Shapes Layer (#7541) Add Image Border / Bounding Box Gallery Examples for both 2D and 3D (#7546) Add right-click indicator to 3D, Roll, Grid, and Square push buttons (#7556) Change naming of 'pan/zoom' mode to 'Move camera' to clarify functionality differences in 2D and 3D (#7569) ENH: adjust layer coordinates in status by _translate_grid (#7584) Add right click indicator to playback icons (#7590) Change ndisplay button to toggle-like to increase discoverability (#7608) [UI] Add Command Palette to the welcome screen (#7613) Fix layout issue in image/surface controls (#7618) Expose additional Camera parameters in GUI with 3D popup widget (#7626) Add 'Extend with Plugins' and 'Contribute to napari' links to the Help menu. (#7645) Restyle visibility icon to clarify different interactions compared to clicking layer (#7657) Add toggle 3D view action (#7721) Add optional font scaling to layer text properties (#7732) Add viewer.fit_to_view(), properly calculate 3D data canvas size, and refactor viewer.reset_view() (#7742) Track layer slider max value (#7756) Maintain 3D camera angles when switching between 2D and 3D views (#7765) Add handedness property to camera and display in GUI (#7770) Revert status bar changes for single active layer (#7775) Add camera orientation parameters to application settings. (#7787) Performance Add numba warmup step when creating empty Shapes Layer (#7541) Add benchmarks for triangulation (#7632) Bug Fixes Fix issues displaying polygons with holes in Shapes (#6654) Fix points data selection for 4D (#6819) Update point add to handle multiple coordinates in data_indices (#7536) Use data.dtype

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