scijava-jupyter-kernel aims to be a Jupyter kernel that integrate well with ImageJ. See here for more details.

Under the hood scijava-jupyter-kernel uses the Beaker base kernel.

Scripting languages supported are :

• Groovy
• Python
• BeanShell
• Clojure
• Java
• JavaScript
• R
• Ruby
• Scala

See also, the collection of notebook examples.

• Install Anaconda
• Install scijava-jupyter-kernel with :

# Add the conda-forge channel
conda config --add channels conda-forge

# Create an isolated environment called `java_env` and install the kernel
conda create --name java_env scijava-jupyter-kernel

• Usage :

# Activate the `java_env` environment
source install java_env

# Check the kernels have been installed
jupyter kernelspec list

# Launch your favorite Jupyter client
jupyter notebook

# or
jupyter lab

Note : It is suggested to install the kernel in an isolated Conda environment (not in the root environment).

• Download the last released JAR file.

• Drop it in your Fiji plugins directory.

• Start Fiji and launch Analyze > Jupyter Kernel > Install Scijava Kernel.

• Set the path to your Python binary.

• Choose a language (for example jython or groovy) or you can choose to install all the available languages.

• Choose a log level.

• Check the kernels have been installed with : jupyter kernelspec list.

• Launch jupyter notebook or jupyter lab and select the kernel you want in the kernel list.

• CI with Travis makes sure the project builds without errors for each new commit.
• All the notebook examples are executed by the kernel during CI with the runipy.py script.
• A Conda package is built for each new release.

Under Apache 2.0 license. See LICENSE.

• Hadrien Mary hadrien.mary@gmail.com