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Image Analysis

Course information

Schedule
Lecture slides
Computer Setup
- Software installation and data download
  - On your local computer
    
    1. Install Fiji
    
    2. Install Python
    
    3. Set up the environment
    
    4. Download the example data
  - Reproducible Research Platform
    
    Using the RRP
    
    Accessing the RRP from outside ETH
- Connecting to the Swiss AI Research Platform
Python Basics
- Python Basics: Exercises

Image Analysis Basics with Fiji

Fiji overview
Fiji practical
Cheat sheet: Fiji basics
Cheat sheet: Fiji macros

Workflows in Python

Basic image handling
- Exercise: image handling
Image processing
- Exercise: image processing
Machine learning for cell segmentation
- Exercise: machine learning for segmentation
Quality control: Segmentation metrics
- Exercise: measuring a segmentation
Feature extraction and measurements
- Exercise: Disaster at the Microscope
Data Analysis: curve fitting
- Exercise: a growth curve from real images

Independent work

Challenge
Homework

Further information

Vocabulary
Further reading
Acknowledgements

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By Marvin Albert and Andreas Cuny. Large parts of the content were adapted with permission from teaching material developed by Aaron Ponti.

© Copyright 2026 ETH Zurich.