MB100P10 - Biological Engineering - ImageJ Intensive Course 2026

[Mgr. Ondřej Šebesta]

Dear students and colleagues,

The 4EU+ Biological Engineering - ImageJ Intensive course 2026 starts on February 19th and will be held every Thursday from 9:00 to 11:20 CET in room 311 at Viničná 7.

We will stream the course on the Meet platform: https://meet.google.com/gsd-jvks-nzs without restrictions. However, online support is limited.

This course aims to show how to work with ImageJ from the basics to the advanced. You don't need any previous knowledge of the software. It is not about image analysis, but we will touch on this topic naturally. Students enrolled in SIS will have to finish their own project in ImageJ to get credits.

The course is up to 20 people in person; regular Charles University and EU4+ students take precedence.

Everybody who would like to attend (including students), please join our Google group - preferably with your CU or Google credentials. I have already added CU emails of the enrolled students to this group.

NOTE: Some people are still in the group from last years. Feel free to unsubscribe.

The materials will be stored on Google Disk.

Program:

19.2.2026 Lesson 1: Basic image handling in FIJI

26.2.2026 Lesson 2: Preparing images for analysis

5.3.2026 Lesson 3: Basic measurements and image segmentation

12.3.2026 Lesson 4: Machine learning techniques and advanced image processing and segmentation

19.3.2026 Lesson 5: CLIJ GPU-accelerated analysis, FIJI customization

26.3.2026 Lesson 6: Introduction to macro language, scripting, and batch processing

2.4.2026 Lesson 7: Programming fundamentals, writing scripts in macro language

9.4.2026 Lesson 8: Writing custom scripts for batch analysis

16.4.2026 Lesson 9: Colocalization analysis

30.4. 2026 Lesson 10: Advanced microscopy techniques, analysis, and image processing

7.5.2026 Lesson 11: Implementation of FIJI in large workflows, using imageJ in a computing cluster

14.5.2026 Lesson 12: Students' projects presentation

30.5 2025 Last day to hand in the final project to pass exams !!!

The lectors are Ondřej Šebesta, Martin Schätz, Roman Leontovič, Jan Pačes, and Barbara Elsnicová

Sincerely,

Mgr. Ondřej Šebesta

-- Mgr. Ondřej Šebesta

Univerzita Karlova v Praze
Přírodovědecká fakulta
Laboratoř Konfokální a Fluorescenční mikroskopie
Viničná 7, 128 44 Praha 2
Telefon: +420 22195 1061
E-mail: ondrej....@natur.cuni.cz

Charles University in Prague
Faculty of Science
Albertov 6, 128 43 Praha 2
www.natur.cuni.cz/en

--

Mgr. Ondřej Šebesta

Univerzita Karlova v Praze
Přírodovědecká fakulta
Laboratoř Konfokální a Fluorescenční mikroskopie
Viničná 7, 128 44 Praha 2
Telefon: +420 22195 1061
E-mail: ondrej....@natur.cuni.cz

Charles University in Prague
Faculty of Science
Albertov 6, 128 43 Praha 2
www.natur.cuni.cz/en