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Write SciJava scripts in Jupyter notebook!
Java Jupyter Notebook Shell
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There is a SciJava Java script engine, but it does not work well with
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README.md

scijava-jupyter-kernel

Travis branch License Anaconda-Server Badge Anaconda-Server Badge Binder

scijava-jupyter-kernel aims to be a polyglot Jupyter kernel. It uses the Scijava scripting languages to execute the code in Jupyter client and it's possible to use different languages in the same notebook.

Some of the supported languages are Groovy (default), Python, Beanshell, Clojure, Javascript, Ruby and Scala.

The kernel has been originally created to work with ImageJ. See here for more details.

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

Binder Usage

Documentation

A documentation is available as a series of notebooks here.

Installation

  • 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 activate java_env

# Check the kernel has been installed
jupyter kernelspec list

# Launch your favorite Jupyter client
jupyter notebook

# or
jupyter lab

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

Development

License

Under Apache 2.0 license. See LICENSE.

Authors

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