COSMAS: a lightweight toolbox for cardiac optical mapping analysis

Jakub Tomek,Zhinuo Jenny Wang,Neil Herring,Gil Bub,Rebecca-Ann Beatrice Burton

doi:10.1038/s41598-021-87402-9

Jakub Tomek, Zhinuo Jenny Wang + Show 3 more

Open Access

https://doi.org/10.1038/s41598-021-87402-9

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Journal: Scientific Reports	Publication Date: Apr 28, 2021
Citations: 21	License type: open-access

Affiliation: University of Oxford, McGill University

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.

Highlights

Optical mapping is widely used in experimental cardiology, as it allows visualization of cardiac membrane potential and calcium transients
This work presents and demonstrates COSMAS, a tool for automated analysis of optical mapping data from cardiac preparations, such as explanted hearts or cardiac cell cultures grown in monolayers
Unlike previous tools for optical mapping data analysis that were implemented in MATLAB11,12, COSMAS is provided both as a MATLAB library and as a Python library, being more accessible to researchers without MATLAB access

Summary

Introduction

Optical mapping is widely used in experimental cardiology, as it allows visualization of cardiac membrane potential and calcium transients. Despite the widespread use of optical mapping techniques in cardiac research, there are surprisingly few standardized tools for their analysis Both available software packages, R hythm[11] and the recently published ElectroMap[12,13] are relatively complex, generally require a large amount of parameters to be set, and are controlled via sophisticated graphical user interface (GUI). We present a new software toolkit COSMAS (COmb-based Software for optical-Mapping AnalysiS) for analysis of cardiac optical mapping data, such as from Langendorff hearts or in vitro cardiac cell cultures It is built around the comb algorithm for detection of APs or CaTs in recordings with known activation rate (e.g. under external pacing or regular sinus rhythm)[15], offering a high quality of processing in a range of common tasks arising in optical mapping of membrane potential or calcium. This is in contrast with Rhythm and ElectroMap, which both require MATLAB (ElectroMap can be run as a stand-alone, but it cannot be adjusted in this form)

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