#JIPipe
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nfdi4bioimage.bsky.social
For anyone who was unable to attend this year’s Boosting Biodata Bootcamp, we’ve compiled the presentations by @nfdi4bioimage.bsky.social speakers:

🔬 Research Data Management for Microscopy – OMERO
👉 doi.org/10.5281/zeno...

💻 Love ImageJ? Advantages of using JIPipe
👉 doi.org/10.5281/zeno...
Group photo of the attendants of the Boosting Biodata Bootcamp.
October 6, 2026 at 8:23 AM
appsysbio.bsky.social
🎉 New role in the team!

Mariia continues with Applied Systems Biology as a technical assistant after completing her Bachelor’s in our group.

Great to have her with us! 🚀

#NewTeamMember #Bioinformatics #ImageAnalysis #JIPipe #AI #HKIJena
May 5, 2026 at 2:04 PM
appsysbio.bsky.social
🎉 Welcome to the team!

Jakob Döge joins Applied Systems Biology as a PhD student in Bioinformatics, working on JIPipe and 3D bioimage analysis.

Wishing him a great start! 🚀

#PhD #Bioinformatics #JIPipe #HKIJena
May 5, 2026 at 12:43 PM
appsysbio.bsky.social
🎉 Our 2026 JIPipe course was a great success!

The enthusiasm and dedication of the participants made it especially enjoyable for us as instructors.

👏 A big thank you to all the excellent participants for their motivation and engagement!

#JIPipe #Training #Science #ImageAnalysis #HKIJena
March 30, 2026 at 11:42 AM
appsysbio.bsky.social
📢 New JIPipe tutorials now on YouTube!🎥

Learn how to build and analyze visual pipelines for bioimage data.
👉 www.youtube.com/@appliedsyst...
Feel free to share your feedback and questions!

#JIPipe #BioimageAnalysis #OpenSource
Applied Systems Biology
www.youtube.com
May 13, 2025 at 8:25 AM
appsysbio.bsky.social
🎉 Girl's and Boy's Day 2025

This year we were delighted to take part in the Forsche Schüler Tag/Boys' and Girls' Day by introducing five interested ninth graders (15-16 years old) to the exciting world of systems biology. 🧪🔬

#STEM #JIPipe #SystemsBiology #ScienceEducation
April 11, 2025 at 2:33 PM
femsjournals.bsky.social
J. P. Praetorius et al. introduce an image-based JIPipe pipeline for automated quantification of #Candida albicans filamentation🧫🖥️
Read more on how this open-source tool enables faster, high-throughput hyphal length analysis:

🔗 buff.ly/ei16oWj
#FEMSYeastRes
July 10, 2025 at 12:02 PM
leibniz-hki.de
Funded PhD position 4/9: Advance image quantification of organ-on-chip-based experiments within JIPipe & benefit from the PhD training program ILRS 2.0.
Apply by 13 Dec.
🎓 lmy.de/tSJYf

#PhDOpportunity #ScienceJobs #LeibnizHKI
A woman sits at a desk with two computer monitors, focused on her work in a bright office; a blurred screen with a scientific graphic is visible in the foreground.
November 29, 2025 at 9:56 AM
longtail-news.bsky.social
Feed: "FocalPlane"
By: Mara Lampert on Tuesday, August 5, 2025
From Click to Code: Reproducibility in Bio-image Analysis
Graphical user interfaces (GUIs) make image analysis more intuitive and accessible, but they also come with a hidden risk: the steps we take aren’t always fully documented or easy to reproduce. To make sure your analysis can be shared, repeated, or even automated later, it’s essential to save your workflows in a structured way. In the following sections, we’ll look into this across several popular platforms, including Napari, Fiji, QuPath, Galaxy, CellProfiler and JIPipe.
focalplane.biologists.com
August 6, 2025 at 7:00 AM
marabuuuu.bsky.social
Ensuring reproducibility in GUI-based bio-image analysis tools can be tricky, so I wrote this new blog post on @focalplane.bsky.social. It highlights features in Napari, Fiji, QuPath, Galaxy, CellProfiler and JIPipe that support workflow saving and sharing. Hope it helps! 🤗🔬👩‍💻Feedback 💛ly welcome!
From Click to Code: Reproducible Bio-image Analysis
Graphical user interfaces (GUIs) make image analysis more intuitive and accessible, but they also come with a hidden risk: the steps we take aren’t always fully documented or easy to reproduce. To mak...
focalplane.biologists.com
August 5, 2025 at 3:13 PM
nfdi4bioimage.bsky.social
Learn how to program advanced data analysis workflows with the visual programming language #JIPipe using the material of the JIPipe Spring course 2026 given by Ruman Gerst and Zoltan Cseresnyes.
To the basic introduction: www.youtube.com/watch?v=KI8r...
To the material: jipipe.hki-jena.de/tutorials/
JIPipe Tutorial (2026) - Basic Introduction - JSC2026
A basic introduction into JIPipe. This is an edited recording from the JIPipe Spring Course 2026 (JSC2026). Please note that we experienced issues with the audio recording. You can find all data…
www.youtube.com
July 28, 2026 at 9:45 AM