Using PyImageJ from Fiji’s Python mode

Fiji includes a Python mode that uses PyImageJ to run Python scripts alongside Fiji. The configuration is available in the latest Fiji release.

Configure Python mode

  1. Start Fiji and select Edit > Options > Python….

  2. Choose a Python environment directory. Use a directory dedicated to this Fiji installation.

  3. Enter any required packages in the Conda dependencies and Pip dependencies fields, one package per line.

  4. Click Build Python environment and wait for the build to finish.

  5. Select Launch in Python mode and click OK.

  6. Restart Fiji when prompted. Fiji will use the configured environment when it starts in Python mode.

Fiji Python mode configuration dialog

The environment definition automatically includes the packages required to connect Python to Fiji, including PyImageJ. The environment is built with Conda and pip, so use the field that matches each dependency.

Updating dependencies

The Python environment is built from the dependency lists in the dialog. If a plugin or script needs a different dependency, update the lists and rebuild the environment.

This integration manages one environment for a Fiji installation. It cannot provide separate dependency environments for multiple plugins, so plugins that require conflicting versions of the same package are not supported together.

Do not rebuild the environment currently being used by Python mode. Restart Fiji in Java mode first, or choose a different target directory, then rebuild.