Course Info

While the skills learned during the course will have broad applications (data analysis, plotting, scripting...), the focus of exercises will be on image analysis and processing topics. Prior knowledge of digital imaging is helpful but not required.

This course is structured in two parts:

  • Introductory Session (October 13-14): Tailored for absolute beginners in Python programming. Participants will start with Python installation and basic syntax, progressing to practical exercises focused on working with digital images and relevant libraries for I/O, measurements, ploting and more. Batch processing of multiple images and an intro to Napari (a Python-based interactive image visualization tool) will also be covered.

  • Advanced Session (October 20-21): This session offers extended hands-on practice, more complex image analysis cases, alternative approaches, and the use of AI tools such as Cellpose for segmentation. This session builds on python skills from the first session. It is ideal for those who completed the introductory session, but also open to participants with basic Python experience. The ability to set up and run a working Python environment is a prerequisite.

    • Applicants may register for either part or both.

    Covered topics:

    • Introductory sessions aimed at installing and familiarizing participants with Conda, Python, and Jupyter Notebook.
    • Fundamentals of Python syntax.
    • Image operations and image processing techniques in Python utilizing essential libraries.
    • AI-based tools for image processing and analysis.
    • Workflows and batch analysis for efficient processing of multiple images and data sets.
    • Image visualization in Napari.
    • Data analysis and visualization using libraries such as Pandas, Seaborn and Matplotlib.

    October 13 - 14 + October 20 - 21, 2025

    BIOCEV, Vestec

    The course is organized by the Imaging Methods Core Facility.

    The course is supported by the National Infrastructure for Biological and Medical Imaging (Czech-BioImaging, Ministry of Education, Youth and Sports – Large Research Infrastructure, LM2023050).