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, Java, 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.
A documentation is available as a series of notebooks here.
- 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 kernel has 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 Fiji release.
-
Add the Scijava Jupyter Kernel update site in Fiji:
- Click Help ▶ Update....
- Click
Manage update sites
. - Select the Scijava Jupyter Kernel checkbox (see also List of update sites).
- Click
Apply changes
and restart Fiji.
-
Launch
Analyze > Jupyter Kernel > Install Scijava Kernel
. -
Set the path to your Python binary.
-
Choose a log level.
-
Check the kernel has been installed with :
jupyter kernelspec list
. -
Launch
jupyter notebook
orjupyter 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.
- A test notebook is executed during CI with nbconvert.
- A Conda package is built for each new release.
Under Apache 2.0 license. See LICENSE.
- Hadrien Mary hadrien.mary@gmail.com