Troubleshooting

This page collects a few known issues and solutions for common problems that users might encounter when using napari. If you are facing an error that is not covered by this page, please check existing issues on the napari repository. If you can’t find what you are looking for, please open a new issue.

Known issues

Plugin errors related to pydantic

napari depends on pydantic, a data validation library. In napari 0.6.0, we dropped support for pydantic v1, changing our minimum required pydantic version to 2.2. This will bring significant speed and functionality advantages to napari. Pydantic v2 was released nearly 2 years ago, so we feel that there has been adequate time for plugins to update (there is a detailed migration guide).
However, there may be plugins that depend on pydantic that have not been updated to work with pydantic 2, but can be installed with napari 0.6.0, because it is not typical to set upper bounds on dependencies. In this case, you will get Import or Runtime errors related to pydantic. If this occurs, you will need to reach out to the developers of the plugin and ask them to update the plugin.
To do this, you can open the Plugin Manager using the Plugins menu: Plugins > Install/Uninstall Plugins... and then click the name of the plugin in the Installed Plugins list. This will take you to the plugin website, where you can look for information on opening an issue or contacting the developers.
Alternately, you can install and use napari 0.5.6 (or lower) and specify "pydantic<2" when installing to continue to use such plugins.

Installed plugin doesn’t show up in Plugins menu

Installed npe2 plugins (this is most plugins!) are not loaded until you restart napari. Try restarting the viewer and see whether this resolves your issue.

Plugin options missing

If you’ve installed a plugin, restarted napari, and some of the plugin’s options are missing e.g. there is no Tools menu or you’re trying to save layers and can’t find the plugin in the listed writers, you might have an auto-converted plugin using the deprecated npe1 engine.

Try turning off the Use npe2 adaptor setting under Preferences -> Plugins -> Use npe2 adaptor and restarting napari. This setting will be removed in version 0.7.0 of napari, so reach out to the plugin developer to update their plugin.

Learn more about this in the adapted plugin guide.

Resetting preferences and settings

Changing napari versions—updating or downgrading—within an environment can cause issues with settings. These issues can manifest as napari failing to start.

Likewise, issues with napari on multiple monitors or with window sizes are also due to settings. These issues can frequently be solved by resetting the settings back to default using the terminal command:

napari --reset

torch + rosetta + napari crashes Python

In some cases, when using napari on Mac M1 using Rosetta you may experience crashing when adding layers or using a script. If you observe this, you should run napari using the native arm64 Python interpreter (see napari#7259.

“module napari has no attribute Viewer”

This may happen when doing an editable install on top of a normal one, or when you have a local file called napari.py.

To fix this, either rename the file or remove all previous napari versions in your environment before installing the editable version.

My image renders as all black/all white

This can happen when the contrast limits are not set correctly. You can reset the contrast limits by right-clicking “contrast limits”, then clicking the “Reset” button in the advanced contrast limits widget shown.

See Adjusting contrast limits for more information on contrast limits.

PermissionError when trying to launch napari on Windows

If you have a PermissionError when trying to launch napari on Windows, it could be due to how numba deals with permissions. Try setting NUMBA_CACHE_DIR to an user-accessible location.

See napari#7288.