Documentation

JIPipe is a visual programming language for ImageJ that allows you to create macros without any programming by just creating a flowchart. In this documentation, you will find information about the basic concepts behind JIPipe, how to create an image analysis pipeline with the JIPipe graphical user interface (GUI), and run your pipeline and review results. You will also find guides how to connect JIPipe with ImageJ and other software.

If you are not familiar with the idea behind JIPipe, we recommend to watch following video:

Here you can find the topics of this documentation:

• Basic concepts

This section explains some basic concepts that are helpful to understand if you want to use JIPipe. Visual programming Explains the basics of visual programming. Batch processing Explains basic concepts about how data is processed within JIPipe. We really recommend to take a look at this documentation.

• Creating pipelines

This section explains the JIPipe user interface, how to create an analysis pipeline, and some concepts behind how analysis pipelines work. Pipeline editor Explains the graph editor user interface, how to create a pipeline, and additional features like the algorithm finder tool. Parameters Explains advanced parameter features. Mathematical expressions Explains the expression parameter type language that is often used for filtering or generating numbers. Graph compartments Explains the concept of graph compartments that allow easy organization of the analysis pipeline into functional units.

• Running pipelines

This section contains documentation that explains how to run a pipeline and review the results. For example, you can run the whole workflow or make use of the cache feature to run single nodes. Running the whole pipeline Explains the Quick Run feature that allows to test and compare different algorithm parameters without recalculating the whole pipeline. Review results Explains how to review results. Use results in external software JIPipe stores outputs in a standardized format that can be easily read with third-party software.

• ImageJ integration

Explains functionality that allows ImageJ to run JIPipe algorithms or pipelines.

• Managing plugins

Explains how to install and manage plugins.

• Standard library

Contains some explanations about the algorithms that are included in the JIPipe standard distribution.

• Extension builder

Explains the extension builder tool

• Command Line Interface

Explains basic concepts about how data is processed within JIPipe. We really recommend to take a look at this documentation.