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Macro programming for everyone!

JIPipe is a graphical batch processing programming language for ImageJ that allows you to create macros without any programming by just creating a flowchart!
Download now Learn how to use it Show examples

Intuitive user interface

JIPipe comes with a modern and easy to use interface that is simple by default, but powerful when needed. All options are logically organized and located where you expect them to be.

Easy to learn

JIPipe comes with helpful tools such as the Algorithm finder that guides you in creating a pipeline by offering compatible processing steps for your current data.

Easy to organize & document

JIPipe allows you to organize your pipelines into compartments and node groups to help you to keep track of your analysis. Furthermore, you can document your pipeline by adding labels, names, and custom descriptions to inputs, outputs, and nodes.

Built on ImageJ

JIPipe is built on the established ImageJ software and comes with commonly used ImageJ functions and plugins, just as CLIJ2 and MorphoLibJ. You can re-use your existing macros and ImageJ2 scripts and create easy-to-use graphical interfaces for them, which will also be available directly within ImageJ via JIPipe's two-way integration.

Easy sharing & extending

JIPipe allows you to export your pipelines as custom nodes that can be installed just like any other ImageJ plugin. Programmers can make use of the powerful API to enhance the feature set even more.

Powerful result evaluation

You can either analyze results directly after processing or load existing results directly into JIPipe. The powerful result analysis tool lets you import data back into ImageJ, or summarize and plot them directly within JIPipe.

Integrated table editor

JIPipe comes with a tool to summarize and concatenate tables without any external tools. The tool can directly import table data generated by ImageJ.

Integrated plot editor

JIPipe comes with a powerful plot builder that supports a multitude of different plot types, such as XY plots, bar charts, histograms, and box plots.

Do you want to try it?

You can try JIPipe right now in three simple steps!
  1. Download ImageJ or open your existing ImageJ installation
  2. Activate the JIPipe update site (Help > Update ...)
  3. Run the JIPipe GUI from within the plugin menu
After starting JIPipe, we recommend you to follow our tutorial or load an example pipeline.

Do you have a question or require some help?

Please do not hesitate to contact us! You can always contact the JIPipe developers via the community, or via E-Mail. If you find a bug, you can also report it directly on GitHub.
Community Send E-Mail Report a bug
JIPipe was developed by Research Group Applied Systems Biology
Head: Prof. Dr. Marc Thilo Figge HKI-Center for Systems Biology of Infection
Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Insitute (HKI)
Adolf-Reichwein-Straße 23, 07745 Jena, Germany