Introduction to Programming for Image Processing

Basic information

The course is tailored to users already familiar with the basics of image processing. It will be focused on automatization, high throughput and basic scripting. Course participants will learn how to create and edit macros in ImageJ and how to write more sophisticated scripts for batch processing. Furthermore, they will learn the basics of image processing in Matlab and Cellpose.

Duration: 2 days + 1 day for optional consultations of individual projects

Registration fee: free of charge

Language: English


Location: Turquoise Auditorium

Speakers: Barbora Hyklová, Štěpán Kortus, Iva Švecová, Jakub Zahumenský

Day 1 / Wednesday / 29. 11. 2023

Morning session: 8:30-11:30 ImageJ

8:30-9:00 Registration
9:00-9:30 Introduction to IEM microscopy group (Barbora Hyklová)
9:30-10:15 Introduction to macros and basic scripting in ImageJ (Štěpán Kortus)
10:15-10:30 Coffee break
10:30-11:30 Batch processing and macros in ImageJ – hands-on session (Štěpán Kortus)

Lunch break: 11:30-12:30

Afternoon session: 12:30-16:00 CellPose

12:30-14:00 Introduction to CellPose (Iva Švecová)
14:00-14:15 Coffee break
14:15-15:30 CellPose – hands-on session (Iva Švecová)
15:30-16:00 Wrap-up

Day 2 / Thursday / 30. 11. 2023

Morning session: 9:00-11:30 workflow automation (ImageJ + CellPose)

9:00-10:15 Using ImageJ and CellPose in an automated workflow (Jakub Zahumenský)
10:15-10:30 Coffee break
10:30-11:30 Workflow automation – hands-on session (Jakub Zahumenský)

Lunch break: 11:30-12:30

Afternoon session: 12:30-16:00 Matlab

12:30-14:00 Introduction to image processing in Matlab (Štěpán Kortus)
14:00-14:15 Coffee break
14:15-15:30 Matlab – hands-on session (Štěpán Kortus)
15:30-16:00 Wrap-up

Day 3 / Friday / 1. 12. 2023

Optional: Discussion of individual projects and data analysis questions. 


Prior Experience with ImageJ: Participants should have a basic familiarity with ImageJ and its fundamental features. They should be comfortable with tasks like image import, basic processing (e.g., brightness/contrast adjustments), and measurements. 

Own notebook: Participants are required to bring their own notebook for hands-on exercises. If you do not have access to a notebook, please inform us in advance, and we will provide you with one. Prior to the event, you will receive a list of required software programs to install for the course.