Back
Back

Introduction to programming for image processing 2026

CourseCzech-BioimagingMicroscopy Published on 06. 01. 2026

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: December 2-4, 2026
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.

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).

Registration

Registration will open a few months before the event date. 

Registration fee

  • In-person participation: 500 CZK (excluding VAT)
  • Online participation: free

In-person registration includes refreshments during coffee breaks and lunch (the first two days only). The activities are identical for both in-person and online participants; however, in-person participation is encouraged, as it offers better opportunities for interaction and direct support. In the event of limited time for questions or discussion, priority will be given to those attending in person.

Capacity is limited to 15 participants on-site and 15 online.


    Contact

    If you have any questions about the course, please contact Iva Švecová at iva.svecova@iem.cas.cz.

    MSMT, Czech-Bioimaging, Euro-Bioimaging logo

    This event is organized by the National Infrastructure for Biological and Medical Imaging (Czech-BioImaging), supported by grants LM2023050 and CZ.02.01.01/00/23_015/0008205.