JIPipe

A graphical batch processing language for image analysis.

https://www.jipipe.org/

Zoltán Cseresnyés, Ruman Gerst, Marc Thilo Figge

Research Group Applied Systems Biology - Head: Prof. Dr. Marc Thilo Figge
https://www.leibniz-hki.de/en/applied-systems-biology.html
HKI-Center for Systems Biology of Infection
Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)
Adolf-Reichwein-Straße 23, 07745 Jena, Germany

The project code is licensed under MIT.
See the LICENSE file provided with the code for the full license.

Downloading JIPipe

You can find the latest release of JIPipe by visiting https://jipipe.hki-jena.de/download/

We also provide snapshot builds that are created directly on the master branch: https://asb-git.hki-jena.de/RGerst/jipipe/-/packages

Project structure

The project consists of following parts:

• JIPipe-Core provides all basic functionality, such as the graph model, projects, and the GUI
• JIPipe-Annotation provides algorithms and data types for handling annotation data.
• JIPipe-Filesystem provides algorithms and data types for handling filesystem data.
• JIPipe-IJ integrates ImageJ data types.
• JIPipe-CLIJ integrates CLIJ2.
• JIPipe-IJ-Algorithms integrates ImageJ algorithms.
• JIPipe-IJ-Multi-Template-Matching integrates the ImageJ multi-template matching plugin.
• JIPipe-IJ-OMERO integrates OMERO.
• JIPipe-IJ-OCR integrates TesseractOCR.
• JIPipe-Filaments filament processing library.
• JIPipe-IJ-Trackmate integrates Trackmate.
• JIPipe-Multiparameters provides algorithms and data types for handling parameter data. It contains the data source algorithms to define parameters.
• JIPipe-Plots provides data types and algorithms for generating plots.
• JIPipe-Python provides a Python-scripting node.
• JIPipe-Tables provides algorithms and data types to handle table data.
• JIPipe-Strings provides algorithms and data types for handling string data.
• JIPipe-Utils provides some helpful utility extensions.
• JIPipe-Forms provides core functions to allow user interaction during pipeline runs.
• JIPipe-Cellpose provides integration of Cellpose
• JIPipe-Omnipose integrates Omnipose.
• JIPipe-IMP in-development library for Photoshop-like image manipulation.
• JIPipe-OpenCV integrates OpenCV (in-development).
• JIPipe-Scene-3D creation and export of 3D scenes.
• JIPipe-Launcher provides a JAR file that launches the JIPipe GUI and CLI from outside of ImageJ

You can use the JIPipe project to setup a development environment, as this project depends on all libraries. Due to internal dependencies, some data types are present in the JIPipe-Core library, but not registered into the JIPipe runtime.

Building JIPipe

You will need following packages:

• Java 21
• Maven

Generate packages

mvn package

You will find the generated *.jar files in ./*/target folders. Copy them into the ImageJ plugins or jar directory. JIPipe requires some dependency libraries that need to be installer. These dependencies also have to be provided. This repository comes with automated tools that downloaded dependencies and to create packages that are ready-to-install.

Generating a package with dependencies

You can find a script build.sh in dist/zip. It will package the output of an existing mvn package run with all necessary dependencies, README files, and licenses into a zip file.

This requires Linux or MacOS. On Windows you can install MSYS2, Cygwin, or use WSL. Also ensure that the zip utility is installed.

# Ensure that the project is built
mvn package

# Navigate into the dist folder
cd dist/zip

# Run the package script
./build.sh

Running JIPipe in an IDE

This repository comes with a project jipipe that allows you to run and debug JIPipe inside your IDE. You just have to run the main() function inside JIPipeLauncher.

You probably will need to add the following option into the Java VM options:

--add-opens=java.base/java.lang=ALL-UNNAMED

This is due to known issues with ImageJ's class patching mechanism (see https://forum.image.sc/t/imagej-legacy-error/23013/10).

Generate JavaDocs (Optional)

mvn javadoc:aggregate

The JavaDoc will be put into the target/site folder.

Troubleshooting

Missing Maven dependencies

Sometimes Maven fails to download certain dependencies if run from CLI. We have experienced that using an IDE can resolve this.

Nullpointer exception on launching in IDE

Clean and compile Maven. Then compile inside the IDE, again.