We are currently working on publishing additional tutorials. Please refer to the outdated tutorials below, which may be helpful even with the changes in JIPipe since their publication.

Tutorials

The following tutorials are recording from JIPipe Spring Course 2025 (JSC2025) event.
JIPipe Tutorials (2025) - JSC2025

Video tutorials recorded in spring 2025 (JIPipe 5.2.0)

Open playlist on YouTube Show files on Zenodo
JIPipe Tutorials (2025) - JSC2025 - Interactive workshop materials

Materials for the interactive part of the tutorial

Download
JIPipe Tutorials (2025) - JSC2025 - Real-world workflows

Workflows based on published pipelines

Neutrophils Cryogels
JIPipe Tutorials (2025) - JSC2025 - Homework

Tasks and workflows for the homework, including the solutions

Homework Solutions
Title Description
Basic Introduction Into Optics & Microscopy - Lecture - JSC2025 A lecture given by Dr. Zoltán Cseresnyés that gives a basic introduction into optics and microscopy in the context of microbiology. Please note that we experienced issues with the audio recording. YouTube Zenodo
Basic Introduction Into Bioimage Analysis - Lecture - JSC2025 A lecture given by Dr. Ruman Gerst that gives a basic introduction into image analysis and establishes a toolbox of commonly used image processing methods. Please note that we experienced issues with the audio recording. YouTube Zenodo
JIPipe Tutorial (2025) - Basic Setup - JSC2025 Explains the download and initial setup of JIPipe and gives a brief overview of the user interface. YouTube Zenodo
JIPipe Tutorial (2025) - Basic Blobs Segmentation - JSC2025 Full interactive tutorial on how to use the JIPipe user interface and create a basic blobs segmentation workflow, showcasing how to import images, apply auto-thresholding, detect particles, and visualize the results. YouTube Zenodo
JIPipe Tutorial (2025) - Intermediate Analysis - Kidney Tissue & Glomeruli - JSC2025 Full interactive tutorial on creating an intermediate-level analysis in JIPipe that segments and analyzes LSFM data from kidneys (Klingberg et al., 2017) involving feature detection, ROI-based filtering, and the branching pathways. YouTube Zenodo
JIPipe Tutorial (2025) - Workflow Organization - Compartments - JSC2025 Full interactive tutorial on how to structure JIPipe workflows using compartments. Requires the kidney analysis workflow (follow earlier tutorial or download the workflow; see below). Also briefly showcases how to annotate graphs with text/comment boxes. YouTube Zenodo
JIPipe Tutorial (2025) - Group Nodes - JSC2025 Brief tutorial on how to create and edit group nodes inside JIPipe. YouTube Zenodo
JPipe Tutorial (2025) - Sharing Nodes & Projects - JSC2025 Full interactive tutorial on how to create and share node templates and how to make use of the project overview to create project-wide parameters. YouTube Zenodo
JIPipe Tutorial (2025) - Batch Processing - JSC2025 Full interactive tutorial on how to convert a single-image analysis workflow into a batch processing pipeline. Requires the blob analysis and kidney analysis workflows (follow previous tutorials or download the workflows; see below). Introduction into text annotations and annotation-guided batch processing. YouTube Zenodo
JIPipe Tutorial (2025) - Path Processing & Exporting Results - JSC2025 Full interactive tutorial on how to automatically export results generated from a JIPipe workflow. Introduction into basic path processing features. YouTube Zenodo
JIPipe Tutorial (2025) - Expressions & Advanced Features - JSC2025 Lecture on how to use JIPipe's expression language and brief overview of other more advanced features. YouTube Zenodo
JIPipe Tutorial (2025) - Workflow Showcase - Neutrophil Segmentation & Tracking - Cellpose - JSC2025 Showcase of a real-world workflow for fully automated segmentation and tracking of neutrophils in transmitted-light images. Usage of Cellpose segmentation and TrackMate 7 tracking nodes. YouTube Zenodo
Homework Discussion - Microscopy - JSC2025 Recording of the microscopy homework discussion. YouTube Zenodo
Homework Discussion - JIPipe - JSC2025 Recording of the JIPipe homework discussion. YouTube Zenodo

Outdated tutorials

Since its release, JIPipe has received significant development, changing how certain features are used. Yet the basic concepts behind the workflow design remains the same, making our old tutorials still useful to some degree.
Here you can find a list of outdated text and video tutorials that over time will be replaced with updated versions.
Old documentation + tutorials

Until we can update our tutorials and documentation for newer JIPipe versions, you can refer to an older version of the guide.

Visit

Video tutorials (old)

There are longer-form tutorials that showcase multiple concepts and shorter tutorials that focus on specific feature of JIPipe.

Full tutorials (old)

JIPipe for ImageJ users

Old tutorial from about 2 years ago. Showcases how to apply an image analysis task (originally published for ImageJ) in JIPipe.

Watch on YouTube Download

Short tutorials (old)

What is JIPipe?

Old video from about 2 years ago. Briefly explains what is JIPipe and why it was developed.

Watch on YouTube Download
Quick guide: user interface

Old video from about 2 years ago. Explains the structure of the JIPipe user interface. Please note that the UI has changed significantly since the release of the video.

Watch on YouTube Download
Quick guide: graph editor

Old video from about 2 years ago. Explains how to use the graph (workflow) editor. Please note that the UI has changed significantly since the release of the video.

Watch on YouTube Download
Quick guide: data caches (running pipelines)

Old video from about 2 years ago. Explains how to run pipelines and store the resuls in memory.

Watch on YouTube Download
Quick guide: batch processing

Old video from about 2 years ago. Explains how to do batch processing.

Watch on YouTube Download