Documentation

This section explains the JIPipe user interface, how to create an analysis pipeline, and some concepts behind how analysis pipelines work.

Batch processing

JIPipe is a tool to create data processing workflows via a graphical language. A special feature of JIPipe processing is always done in batches, meaning that workflows are always designed to scale for large amounts of data without the need of external scripts or major changes in a pipeline.

The JIPipe graphical language is graph-based where nodes represent data processing algorithms and edges represent that data is transferred from an algorithm output to another algorithm’s input.

An example is the application of a gaussian filter to an image after loading it:

graph LR; A[File] --> B[Load image] B --> C[Apply gaussian]

To design efficient and scalable pipelines yourself, it is a good idea to look into the JIPipe data model.

Graph compartments

A common issue with graphical programming languages is that larger pipelines are hard to navigate. Another issue with such languages is that it is hard to separate functional units for easier readability.

JIPipe solves both issues with the concept of strongly separated graph components that group a set of algorithms together. Components only can interact via special interface algorithms, making it easier to structure the pipeline.

Please take a look at our graph compartment documentation for more information.

User interface overview

The JIPipe user interface is designed around managing an analysis project. A project contains all information to run an analysis, outside of the input data and can be saved into JSON files. The user interface is separated into three sections:

  1. The project menu contains all operations for the current project / window. It allows you to open/save projects, access and modify graph compartments, manage plugins, and run the analysis
  2. The tab bar allows you to switch between different interfaces associated to the current project. You can close thabs by clicking the x icon. If a tab contains some data that will be lost after closing it, you will have to confirm the action. If no question is asked on closing a tab, you will be able to open it later again without losing data.
  3. The current content depends on the selected tab

You can also close a tab by clicking it with the middle mouse button.

Further reading