This Indico installation shall not be used to organise MPI-CBG courses and events from beginning of 2024 on. Please use MPG Indico instead.
17-21 October 2022
Europe/Berlin timezone

Registration deadline: 29 September 2022

Course aim:

This 5-day course will introduce you to the basics of image data science using Python, napari and Jupyter, enabling you to develop reproducible image analysis workflows using state-of-the art data science methods. This will allow you to differentiate objects such as cells with different phenotypes and quantify their properties such as shape, size, expression levels. Intermediate coding skills expected.

The course will take place in person at CSBD, SR Top Floor.

We will inform you after 29 September if we can offer you a space in this course!

SR Top Floor


Robert Haase, Marcelo Zoccoler, Johannes Müller and Till Korten, DFG Cluster of Excellence “Physics of Life”, TU Dresden

Each part of the course contains some theoretical presentations, short exercises to apply new knowledge and a long exercise to start combining the tools and tackle more real life analysis.

All days 09:00-17:00.

  • Day 1: A brief introduction to Bio-Image Analysis: from images to knowledge! Interactively explore your images in Jupyter notebooks, visualize 3D images with napari and start exploring image processing techniques like filtering with scikit-image.
  • Day 2: A deeper plunge into the core concepts of image analysis with semantic and instance segmentation, and feature extraction. Powered with GPU acceleration!
  • Day 3: Data science and biostatistics. Process tables of measurements using pandas in order to calculate and plot descriptive statistics and run unsupervised machine learning techniques for object classification and clustering.
  • Day 4: Good scientific practice regarding code sustainability and usability, e.g., write code that you (and others) can still understand and use after 6 months. To help you distribute your code to others, you will learn how to create a napari plugin from a python function.
  • Day 5: Bring your own data. We will help you to apply your new knowledge to your own data.


Get your laptop ready for the course. You will need it to perform all the hands-on sessions and exercises.

Before the course:

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