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

Registration fee: free of charge

Language: English

Programme

Location: Turquoise Auditorium

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

Day 1 / Wednesday / 13. 11. 2023

Introduction, macro recording and editing in ImageJ

Day 2 / Thursday / 14. 11. 2023

Writing a complex macro for batch processing – automatic data import, cell segmentation, particle tracking, measurements, export in organized format

Cell segmentation using CellPose

Day 3 / Friday / 15.11. 2023

Introduction to Matlab for image processing: Matlab basics, image import, image registration, combining images from two modalities (SMLM and WF), writing scripts

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 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.