Welcome note ImageJ course

[Mgr. Ondřej Šebesta]

Dear students,

The intensive ImageJ course starts tomorrow at 9:00 in room 311 at Viničná 7. This course aims to show how to work with ImageJ from basics to advanced. This course is not about image analysis but we will touch this topic naturally. Students enrolled in SIS will have to finish with own project in ImageJ to get credits.

The course is up to 20 people in person, and 7  chairs are still available.

We will stream the course on the meet platform: https://meet.google.com/ync-sqdz-ocy without restrictions. However, online support is limited.

If anybody else would like to attend, please join our Google group. No previous knowledge of the software is necessary.

The materials will be stored on Google Disk.

Here is the final program:

Lesson 1, 22.2.2024, Basic image handling in FIJI
Lesson 2, 29.2.2024, Basic measurements and image segmentation
Lesson 3, 7.3.2024, Preparing images for analysis
Lesson 4, 14.3.2024, Colocalization analysis
Lesson 5, 21.3.2024, Introduction to macro language, scripting, and batch processing
Lesson 6, 28.3.2024, Programming fundamentals, writing scripts in macro language
Lesson 7, 4.4.2024, Writing custom scripts for batch analysis
Lesson 8, 11.4.2024, CLIJ GPU accelerated analysis, FIJI customization
Lesson 9, 18.4.2024, Machine learning techniques and advanced image processing and segmentation
Lesson 10, 2.5.2024, Advanced microscopy techniques analysis and image processing
Lesson 11, 9.5.2024, Implementation FIJI in large workflows, using imageJ in a computing cluster
Lesson 12, 16.5.2024, Students projects presentation

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

Sincerely,

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]

Dear students and colleagues,

The 4EU+ Biological Engineering - ImageJ Intensive course 2025 starts on February 20th 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/dbz-qnhw-cvd 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.

We will stream the course on the meet platform: https://meet.google.com/dbz-qnhw-cvd without restrictions. However, online support is limited.

Everybody who would like to attend (including students), please join our Google group - preferably with your CU credentials.

NOTE: some people are still in the group from last year. Feel free to unsubscribe.

The materials will be stored on Google Disk.

The program:

Lesson 1, 20.2.2025, Basic image handling in FIJI
Lesson 2, 27.2.2025, Basic measurements and image segmentation
Lesson 3, 6.3.2025, Preparing images for analysis
Lesson 4, 13.3.2025, Colocalization analysis
Lesson 5, 20.3.2025, Introduction to macro language, scripting, and batch processing
Lesson 6, 27.3.2025, Programming fundamentals, writing scripts in macro language
Lesson 7, 3.4.2025, Writing custom scripts for batch analysis
Lesson 8, 10.4.2025, CLIJ GPU accelerated analysis, FIJI customization
Lesson 9, 17.4.2025, Machine learning techniques and advanced image processing and segmentation
Lesson 10, 24.4.2025, Implementation FIJI in large workflows, using imageJ in a computing cluster
Lesson 11, 15.5.2025, Students projects presentations

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