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.

Class diagram of the CyAn toolbox

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.

Plots of different data that can be measured with CyAn, including single cell and single molecule data, as well as colony morphology

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.


The CyAn project is available through the BioFrontiers Institute’s Gitlab instance.


J. W. Tay and J. C. Cameron. CyAn: A MATLAB toolbox for image and data analysis of cyanobacteria. bioRxiv (2020)