COSMAS: a lightweight toolbox for cardiac optical mapping analysis

Abstract

Abstract Optical mapping is widely used in experimental cardiology, as it allows visualization of cardiac membrane potential and calcium transients. However, optical mapping measurements from a single heart or cell culture can produce several gigabytes of data, warranting automated computer analysis. Here we present COSMAS, a software toolkit for automated analysis of optical mapping recordings in cardiac preparations. COSMAS generates activation and conduction velocity maps, as well as visualizations of action potential and calcium transient duration, S1-S2 protocol analysis, and alternans mapping. The software is built around our recent ‘comb’ algorithm for segmentation of action potentials and calcium transients, offering excellent performance and high resistance to noise. A core feature of our software is that it is based on scripting as opposed to relying on a graphical user interface for user input. The central role of scripts in the analysis pipeline enables batch processing and promotes reproducibility and transparency in the interpretation of large cardiac data sets. Finally, the code is designed to be easily extended, allowing researchers to add functionality if needed. COSMAS is provided in two languages, Matlab and Python, and is distributed with a user guide and sample scripts, so that accessibility to researchers is maximized.