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This project contains example code for working with ImageJ and SciJava.

JUPYTER NOTEBOOKS

Binder

The easiest way to get started with the ImageJ and SciJava APIs is via the ImageJ Jupyter notebooks, located in the notebooks subfolder of this repository.

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

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.

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

  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.

Learn more about Jupyter Notebook on its web site.

JAVA PROJECTS

Open in Gitpod

For the type-safety-inclined, this repository also contains Maven projects written in Java, located in the maven-projects subfolder of this repository.

Use the "Open in Gitpod" button above to run the (non-GUI) Java projects on the cloud using Gitpod, with no local installation necessary.

You can import these projects into your favorite IDE:

  • Eclipse: File > Import > Existing Maven Projects
  • NetBeans: File > Open Project
  • IDEA: File > Open Project... (select pom.xml)

Or build and run from the command line:

mvn
cd maven-projects/simple-commands
mvn -Pexec -Dmain-class=GradientImage

LICENSING

To the extent possible under law, the ImageJ developers have waived all copyright and related or neighboring rights to this tutorial code.

See unlicense.org for details.

SEE ALSO

Directory Layout (not final)

ImageJ Tutorial Map