Due to reaching capacity for in-person participation, registration is now only available for online attendance. Thank you for your understanding. 

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: 3 days

Language: English

Programme

Location: Turquoise Auditorium

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

Day 1 / Wednesday / 27. 11. 2024

• Introduction, macro recording and editing in ImageJ
• Writing a complex macro for batch processing – automatic data import, cell segmentation, measurements, export in organized format

Day 2 / Thursday / 28. 11. 2024

• Script automation, ImageJ customization
• Cell segmentation using Cellpose and integration of Cellpose into the workflow
• Demonstration of a complex ImageJ/Cellpose workflow

Day 3 / Friday / 29.11. 2024

• Optional: Discussion of individual projects and data analysis questions. 

Requirements

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 laptop: 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 required software programs to install for the course.