Intuitive programming

JIPipe provides a visual programming language into ImageJ that was designed as full replacement for writing macros or Python scripts. Just arrange the operations of your workflow into a flow chart and let JIPipe automatically handle data and metadata management, parallelization, type conversions, error validation, and export of results.

Find and manage nodes

JIPipe helps you to learn about the over 1000 available nodes by organizing them into searchable menus and by integrating the Algorithm finder that guides you in creating a pipeline by offering compatible processing steps for your current data. All documentation, including relevant papers are accessible within JIPipe.

Organize and document your pipelines

IPipe allows you to organize your pipelines into compartments and groups to help you to keep track of your analysis. Keep track of important nodes via an integrated bookmark system. Furthermore, you can document your pipeline by adding comment nodes, and set custom labels, names, and descriptions.

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.

Plugin support

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 Java API to enhance the feature set even more and publish extensions just as any ImageJ plugin.

Review results

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.

Advanced table processing

JIPipe comes with functions to modify and process tables. These includes table processing nodes and a graphical tool for editing tables interactively.

Advanced plotting

JIPipe includes both plotting nodes and an interactive plot builder based on JFreeChart that supports a multitude of different plot types, including XY plots, bar charts, histograms, and box plots