Pipeline editor

This guide is also available as video tutorial.

The graph editor (pipeline editor) allows you to edit the processing steps of a graph compartment. Its user interface is separated into three sections:

  1. The analysis graph contains the processing steps (also referred as algorithms)
  2. The settings panel shows the properties of the currently selected algorithms
  3. The toolbar allows you to add more algorithms into the graph, navigate to existing algorithms, change some behavior settings of the graph editor, and create screenshots

User interface overview

Analysis graph

The analysis graph contains algorithms that are represented by rectangles. The algorithm graph area will automatically grow depending on where you place the algorithms. Scroll bars will appear if the graph area is larger than the available screen size.

An alternative to using the scroll bars is to hold the middle mouse button while dragging the your mouse.

Algorithms read data from their input slots and output the results into the output slots. There are some algorithms that do not have input slots - they produce output based on their current parameters. The algorithm user interface has three sections:

  1. Input slots are located on the top of the algorithm UI. Each slot has a unique name that is displayed below the arrow. The arrow opens a menu that allows you to make/modify connections or change other options specific to the slot. Depending on the algorithm, a + button is created that allows you to add more slots.
  2. The drag area allows you to move the algorithm around. Move your mouse pointer over the area and drag your mouse while holding the 🖱 left mouse button. On clicking the button, a menu will open that contains some algorithm options. Alternatively you can right-click the drag area to open this menu.
  3. Output slots are located on the bottom and allow you to connect your output data to the input of another algorithm.

Any output data is always saved automatically by JIPipe. After generating the final output data, there is no need to connect it to any input.

User interface overview

Slot connections

You can connect two slots by clicking the or button of a slot and by selecting the source/target slot. Input slots can only receive one connection, while outputs can be distributed to as many inputs as you wish. The selection menu shows all available target slots and its sorted from the nearest to the slot that is furthest away.

A connection is shows as line between the connected slots. The color of the line indicates if this connection is valid or invalid depending on the data types of the source and target.

Hover with your mouse over a slot’s name to show information about its data type.

Slot options

The slot context menu opened by or contain additional entries to managing connections.

Algorithm settings

The algorithm settings are displayed on the right-hand side and contain all settings of the selected algorithm. There are usually four categories:


The toolbar contains functions to add new algorithms into the graph, navigate to existing algorithms or search the list of available algorithms, and functions to control the algorithm graph display.

Toolbar UI

Additional tools

View modes

The graph can be displayed in different view modes. There are currently three modes integrated:

Nodes arrangements are saved for each view mode separately. Graphs will remember the current view mode.

You can change the default view mode via Project > Application settings > Graph Editor > Default view mode

Here you will find a preview of all view modes with the same graph. The screenshots all have the same size.

Vertical Vertical (compact) Horizontal