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Course Material

00 - Introduction to BoBiAC
01 - Getting Started with Python
02 - Python Basics
- The Python Basics Notebook
- Errors Everywhere
03 - Introduction to Digital Images
- Working with Bioimages in Python
04 - Image Segmentation
05 - Spot Detection
06 - Object Classification
- Ilastik for Object Classification
07 - From Images to Data
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

00 - Introduction to BoBiAC

00 - Introduction to BoBiAC#

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01 - Getting Started with Python

By Federico Gasparoli, PhD - federico@hms.harvard.edu (federico.gasparoli@gmail.com)
Materials:
- Federico Gasparoli, PhD - federico@hms.harvard.edu (federico.gasparoli@gmail.com)
- Eva de la Serna, PhD - eva_delaserna@hms.harvard.edu
- Max Brambach, PhD - max_brambach@hms.harvard.edu

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