Self-driving, multi-scale image analysis
Self-driving, multi-scale image analysis software is an open-source collection of Python and Matlab code to analyse custom multi-scale light-sheet microscope data from continuous, long-term, simultaneous low- and high-resolution imaging.
If you use this code, please cite our paper: "Imaging of cellular dynamics from a whole organism to subcellular scale with self-driving, multiscale microscopy." Nat Methods 22, 569–578 (2025). by Stephan Daetwyler, Hanieh Mazloom-Farsibaf, Felix Y. Zhou, Dagan Segal, Etai Sapoznik, Jill M. Westcott, Rolf A. Brekken, Gaudenz Danuser and Reto Fiolka https://doi.org/10.1038/s41592-025-02598-2
The Github repository for all the described code is here: https://github.com/DaetwylerStephan/multi-scale-image-analysis/
Test data to run the scripts is available on Synapse https://doi.org/10.7303/syn61795850 and Zenodo: https://doi.org/10.5281/zenodo.12791724
Getting started and installation
Microscope characterization
Low-resolution analysis
High-resolution analysis
Data visualization
Python API references