README.md

JUPYTER NOTEBOOKS

Welcome to the Jupyter notebook tutorials for the ImageJ and SciJava APIs. Here you will find a variety of notebooks detailing different use cases, examples and demonstrations of ImageJ, SciJAva, ImageJ-Ops and more. While we arranged the notebooks from introduction to more specific and advanced topics, you can start anywhere you like.

Use the "launch binder" badge above to try the Jupyter notebooks on the cloud using Binder, with no local installation necessary.

To run the notebooks locally, simply install the Jupyter software and clone this repository.

There is more than one way to install Jupyter, but here is the procedure we recommend to get started quickly with Jupyter and the ImageJ tutorials:

1. Install Miniconda.
2. Clone this imagej/tutorials repository.
3. Open a console and cd to your cloned working copy.
4. conda env create -f environment.yml to create a conda environment with the dependencies these notebooks need.
5. conda activate scijava to activate the environment.
6. jupyter notebook to launch Jupyter Notebook in a web browser window.
7. In the browser, click into notebooks, then click on the ImageJ-Tutorials-and-Demo.ipynb notebook to open it.

The introductory notebooks use the Groovy kernel from BeakerX. Several other JVM-based kernels are usable as well, including Clojure, Java, Kotlin and Scala.

There are also notebooks using the standard Python kernel plus the pyimagej package, enabling use of ImageJ from Python programs.

Learn more about Jupyter Notebook on its web site.

Notebooks directory layout (not final)