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Preparation of the session
Python code in Jupyter notebooks
Pitfalls when working with Jupyter notebooks
Bioimage Analysis in Jupyter Notebooks
Cropping images

Multi-channel image data

Inspecting 3D image data with pyclesperanto

Filter overview

Understanding filters visually

Background removal filters

Connected component labeling

Voronoi-Otsu-labeling

Image Segmentation with CellPose-SAM

Quantitative image analysis

Visualization of measurements

Cell Rounding Assay Analysis

How process files in a folder

Statistical testing

AI-assisted Notebook generation

Simulation of image formation + image restoration

Cell Segmentation Using the Watershed Algorithm

Interactive histogram

Download slides

License CC-BY 4.0

Site Navigation

Preparation of the session
Python code in Jupyter notebooks
Pitfalls when working with Jupyter notebooks
Bioimage Analysis in Jupyter Notebooks
Cropping images

Multi-channel image data

Inspecting 3D image data with pyclesperanto

Filter overview

Understanding filters visually

Background removal filters

Connected component labeling

Voronoi-Otsu-labeling

Image Segmentation with CellPose-SAM

Quantitative image analysis

Visualization of measurements

Cell Rounding Assay Analysis

How process files in a folder

Statistical testing

AI-assisted Notebook generation

Simulation of image formation + image restoration

Cell Segmentation Using the Watershed Algorithm

Interactive histogram

Download slides

License CC-BY 4.0

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Bio-Image Analysis @ EMBL Heidelberg 2026

Preparation

Preparation of the session

Jupyter notebook basics

Python code in Jupyter notebooks
Pitfalls when working with Jupyter notebooks

Image file handling and visualization

Bioimage Analysis in Jupyter Notebooks
Cropping images
Multi-channel image data
Inspecting 3D image data with pyclesperanto

Image filtering

Filter overview
Understanding filters visually
Background removal filters

Image segmentation

Thresholding
Connected component labeling
Voronoi-Otsu-labeling
Image Segmentation with CellPose-SAM

Quantitative measurements

Quantitative image analysis
Visualization of measurements
Cell Rounding Assay Analysis
How process files in a folder

AI for code generation

BiA-Bob
Statistical testing
AI-assisted Notebook generation

Extras

Simulation of image formation + image restoration
Cell Segmentation Using the Watershed Algorithm
Interactive histogram

Links

Download slides
License CC-BY 4.0
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By Robert Haase

© Copyright 2026.

Last updated on None.