CyAn: A toolbox for analysis of microscope images of cyanobacteria
CyAn is a toolbox written in MATLAB to analyze time-lapse microscope images of cyanobacteria cells. CyAn was written to be easy-to-use, only requiring basic programming knowledge.
CyAn was built using a modular approach. The toolbox defines two main classes: CyTracker, which handles the image analysis and tracking, and DataAnalyzer, which implements a basic data structure to hold tracked data and common analysis routines.
The computational algorithms can identify individual cells and sub-cellular components, as well as track cell growth and division to form cell lineages. More details of CyAn can be found through our bioRxiv submission.
CyAn has already been used to study the life cycle of a bacterial microcompartment, the carboxysome, which is essential for carbon fixation in cyanobacteria, as well as showing how mechanical forces play a role in the regulation of photosynthesis. More details on these projects are available here.
Code
The CyAn project is available through the BioFrontiers Institute’s Gitlab instance.