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Course Material
00 -
Introduction to BoBiAC
01 -
Getting Started with Python
Introduction to Python
Jupyter Notebooks and juv
Getting started with uv
Glossary
02 -
Python Basics
The Python Basics Notebook
Errors Everywhere
03 -
Introduction to Digital Images
Working with Bioimages in Python
04 -
Image Segmentation
Classical Methods
Classical Segmentation
Machine Learning Methods
Introduction to Ilastik
Ilastik for Pixel Classification
From Ilastik Masks to Labels
Deep Learning Methods
Introduction to Cellpose
Cellpose in Python
Retraining Cellpose on Custom Data
05 -
Spot Detection
Introduction to Spotiflow
Spotiflow in Python
Finetuning or Training Spotiflow on Custom Data
06 -
Object Classification
Ilastik for Object Classification
07 -
From Images to Data
Measurement Pipeline
Nested Measurements
Background Correction
08 -
Introduction to Spatial Analysis
Intensity-based Colocalization
Pearson’s correlation coefficient
Manders’ Colocalization Coefficients
Spatial Statistics
Notebook 1: Does a protein cluster?
Notebook 2: Do two different protein clusters co-localize?
BoBiAC Exercises
BoBiAC Exercises
Course Materials Downloads
Downloads
Links
BoBiAC
uv
juv
pyrunner
Core for Imaging Technology & Education (CITE)
Past Editions
2025 Edition
Contributors
Federico Gasparoli, PhD
Eva de la Serna, PhD
Max Brambach, PhD
Amelie Andreas
Index
