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 preprint: “Imaging of cellular dynamics in vitro and in situ: from a whole organism to sub-cellular imaging with self-driving, multi-scale microscopy” 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://www.biorxiv.org/content/10.1101/2024.02.28.582579v1

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

• Getting started
  • Requirements
  • Get ready
  • Software installation
  • Running and editing functions with PyCharm
  • Test data location
  • Troubleshooting

Microscope characterization

• PSF analysis
  • Running the Python script
  • Testdata set for PSF characterization
• Shannon Entropy Analysis
  • Running the Python script
  • Output
  • Testdata set for PSF characterization

Low-resolution analysis

• Data stitching
  • Our stitching pipeline
  • Output
  • Test dataset
  • Alternatives
• Low-resolution segmentation
  • Setting up segmentation
  • Output
  • Test data for low-resolution visualization
• Hopkins Statistics Analysis
  • Zebrafish volume approximation
  • Hopkins statistics calculation with Matlab
  • Matlab compiled version
  • Test data for cell shape feature analysis

High-resolution analysis

• High-resolution segmentation
  • Our pipeline
• Cell Shape Feature Analysis
  • Running the Matlab code
  • Matlab compiled version
  • Test data for cell shape feature analysis
• Cell Curvature Analysis
  • Matlab code
  • Matlab compiled version
  • Test data for cell curvature analysis

Data visualization

• Data visualization
  • Generate a custom colormap for labels
  • Visualization of low-resolution data
  • Test data for low-resolution visualization
  • Visualization of high-resolution data
  • Test data for high-resolution visualization

Python API references

• multiScaleAnalysis

Indices and tables

• Index

• Module Index