JIPipe Spring Course 2026 (concluded)

Information for the concluded JIPipe Spring Course 2026 (JSC2026)

2026-03-27

Required hardware and software

We will provide you with a seat that comes with a PC, screen, mouse, and keyboard. If you want to use your own hardware (laptop), please follow our recommendations:

  • Operating system: Windows 10/11 or Linux (macOS is technically supported, but we cannot 100% promise that it will work perfectly)

  • System memory (RAM): At least 16GB

Please download the correct JIPipe version: please go with the latest JIPipe 6.0.0 snapshot that you can find here: https://jipipe.hki-jena.de/download-snapshot

We will need features that are only present in JIPipe 6.

A part of the course will be the download and installation of JIPipe.

Important: We recommend you do not install JIPipe as an ImageJ plugin into your existing Fiji - JIPipe requires a special installation procedure if you install it as plugin. Please go with the prepackaged standalone installations that are prominently featured on the homepage.

Interactive workshop data

Provided through the Google Drive

Direct download: https://drive.google.com/file/d/141gzkkit91RjgYY30glrMTHb0mbJEq3v/view?usp=drive_link

Additional data (may or may not be needed): https://drive.google.com/file/d/1dtolrvTHcvVEU3UPUNXNDKByvkNjW1H9/view?usp=sharing

Advanced workshop data

Provided through the Google Drive

Direct download: https://drive.google.com/file/d/1QqWZoRWhGDWrFngi6e-g8EEnlT6_qdut/view?usp=drive_link

Homework

We highly encourage you to work together with others to be able to work efficiently and learn from each other!

Also do not underestimate the Microscopy homework!

If you have questions, we will gladly help you!

Additional infos

  • The batch-processing datasets were organized so there are no blank input images and all inputs have 5 channels

  • The compartment specification is a suggestion of what nodes may be within each compartment, based on the published workflow. Exact file names, colors, etc. are up to you - just ensure that the tasks are fulfilled

  • Microscopy question #7 is a bonus question

  • In question 1.5 we meant to say "cell membrane", NOT nucleus.

  • Do not forget to check out the "Additional information" PDF file that clarifies some patterns

  • Do not forget that there's a translation table from ImageJ to JIPipe in the document

  • Please note that the marker-based segmentation needs segmented nuclei as marker and in JIPipe needs a connected components labeling

  • New: Since 26.03.2026 : An updated JIPipe 6.0.0 snapshot version was uploaded which allows to simplify the creation of exporter paths. You can access the feature through the new "Build" button

  • Image analysis task 2: The inputs_full, inputs_reduced, inputs_minimal folders should be the starting point (input folder). No elaborate filtering except for TIFF files is needed.

  • Image analysis task 3 is a pure organization/project organization task - you do not need additional statistics and operations - just follow what the tasks table says. The specifications are based on the real-world workflow and are only a hint on what actually can be done in addition to the parts you built up in Task 1 and Task 2. If you choose to do the additional visualizations and outputs in Task 3, you'll receive up to 2 bonus points.

Course concluded

Thank you for participating in our course!

All material will be soon published as tutorials.