15. 01. 2025
Basic information
This course is aimed at participants familiar with the basics of image processing, who want to automate their analysis using scripting. We will work with ImageJ macro language and use it to create a workflow for segmentation, batch processing and analysis of fluorescence microscopy images. In the second part of the course, we will introduce Cellpose, a machine learning algorithm for cell segmentation, demonstrate its use through command line and ImageJ plugin, and incorporate its output into the ImageJ workflow.
No previous programming knowledge is expected, and the course will therefore also briefly introduce basic programming concepts, such as variables, for loops and conditionals (if-else statements). Most of the sessions will be hands-on, and the last day will be dedicated to individual consultations of user projects and questions.
Date: November 12-14, 2025
Duration: 3 days
Language: English
Requirements: bring your own laptop
The course is organized in hybrid form and it is possible to join either in-person or online.
Target audience
The course is primarily aimed at participants with some experience with ImageJ and basic understanding of bioimage analysis. We expect no or minimal knowledge of programming.
Program
Location: Turquoise Auditorium
Speakers: Štěpán Kortus, Iva Švecová, Barbora Hyklová
Day 1 / Wednesday / 12.11.2025
Morning session: 9:00-11:30
8:45-9:00 Registration
9:00-9:20 Introduction of the IEM Microscopy service centre and Czech-Bioimaging
9:20-10:15 Overview of the segmentation workflow and the macro record function
10:15-10:30 Coffee break
10:30-11:30 Workflow continuation, converting recorded commands into an ImageJ macro
Lunch break: 11:30-12:30
Afternoon session: 12:30-16:00
12:30-13:55 Fundamental concepts in batch processing
13:55-14:15 Coffee break
14:15-16:00 Writing a batch script for image segmentation
16:00-16:30 Questions and wrap-up
Day 2 / Thursday / 13.11.2025
Morning session: 9:00-11:30
9:00-10:00 Introduction to Cellpose
10:00-10:15 Coffee break
10:15-11:30 Cellpose in batch mode, training your own model
Lunch break: 11:30-12:30
Afternoon session: 12:30-15:30
12:30-13:00 Integrating Cellpose into batch processing workflows
13:00-14:00 ImageJ/Fiji tips and tricks
14:00-14:20 Coffee break
14:20-15:15 Building complex workflows, workflow integration
15:15-15:30 Questions and wrap-up
Day 3 / Friday / 14.11.2025
Optional: Discussion of individual projects and data analysis questions.
Requirements
Participants are required to bring their own laptop for hands-on exercises. If you do not have access to a laptop, please inform us in advance, and we will provide you with one. Prior to the event, you will receive a list of the required software programs to install for the course.
Please make sure that all required software is installed and works prior to the workshop, especially if your laptop runs macOS or Linux (we work mostly with Windows and are therefore not as familiar with the other operating systems, therefore troubleshooting during the course is difficult).
