CyAn: Cyanobacteria image analysis toolbox
Cyanobacteria are ecologically important microbes responsible for the earth’s oxygen-rich atmosphere. It is currently estimated that cyanobacteria produce about 20% of the earth’s oxygen, yet only comprise less than 1% of the earth’s biomass. This fact highlights their efficient photosynthetic processes. Hence, they are being heavily developed for industrial applications, including the production of biofuels, as well as for food production.
A computational approach to studying individual cyanobacteria
The Cameron Lab at CU Boulder is one of the first to demonstrate live imaging of cyanobacteria using time-lapse fluorescence microscopy. However, the resulting images were difficult to analyze by hand due to the number of objects that needed to be tracked.
I worked with the Cameron lab to develop software to analyze the resulting images. Using this toolbox, we can analyze the growth and physiology of bacterial cells at different length scales, including single cells, to whole colonies, to entire populations.
A white paper on this toolbox has been uploaded to bioRxiv:
- Tay and Cameron CyAn: A MATLAB toolbox for image and data analysis of cyanobacteria. bioRxiv (2020).
This toolbox has been used to make a number of significant discoveries on cyanobacteria physiology:
- Moore et al. Mechanical regulation of photosynthesis in cyanobacteria. Nature Microbiology 5, 757-767 (2020)
- Hill et al. Lifecycle of a cyanobacterial carboxysome. Science Advances 6, eaba1269 (2020)
Additionally, we are working on a manuscript which shows how cyanobacteria populations can survive photodamaging light conditions:
- Tay and Cameron. Fluorescence microscopy reveals heterogeneity in cyanobacterial survival of photodamage. Draft in preparation (2021).