This repository contains a collection of Python Jupyter notebooks explaining bio-image analysis to a broad audience, focusing on life-scientists working with three dimensional fluorescence microscopy for analyzing cells and tissues. The content is available at

https://haesleinhuepf.github.io/BioImageAnalysisNotebooks

It is maintained using Jupyter lab and build using Jupyter book.

To edit this book, install depencencies like this:

pip install pyclesperanto-prototype
pip install jupyterlab
pip install jupyter-book
pip install jupyterlab-spellchecker

git clone https://github.com/haesleinhuepf/BioImageAnalysisNotebooks
cd BioImageAnalysisNotebooks
jupyter lab

To build the book, you can run this from the same folder (tested on MacOS only):

chmod u+x ./build.sh
./build.sh

To clear the build, e.g. before committing using git, run this:

chmod u+x ./clean.sh
./clean.sh

R.H. acknowledges support by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy—EXC2068–Cluster of Excellence Physics of Life of TU Dresden. This project has been made possible in part by grant numbers 2021-240341, 2021-237734 and 2022-252520 from the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation.