COSMAS: a lightweight toolbox for cardiac optical mapping analysis

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...

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Autores principales:	Jakub Tomek, Zhinuo Jenny Wang, Rebecca-Ann Beatrice Burton, Neil Herring, Gil Bub
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5de9830f1263460b9808cc02bb4fe0c6
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spelling	oai:doaj.org-article:5de9830f1263460b9808cc02bb4fe0c62021-12-02T17:39:19ZCOSMAS: a lightweight toolbox for cardiac optical mapping analysis10.1038/s41598-021-87402-92045-2322https://doaj.org/article/5de9830f1263460b9808cc02bb4fe0c62021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-87402-9https://doaj.org/toc/2045-2322Abstract 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.Jakub TomekZhinuo Jenny WangRebecca-Ann Beatrice BurtonNeil HerringGil BubNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-17 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jakub Tomek Zhinuo Jenny Wang Rebecca-Ann Beatrice Burton Neil Herring Gil Bub COSMAS: a lightweight toolbox for cardiac optical mapping analysis
description	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.
format	article
author	Jakub Tomek Zhinuo Jenny Wang Rebecca-Ann Beatrice Burton Neil Herring Gil Bub
author_facet	Jakub Tomek Zhinuo Jenny Wang Rebecca-Ann Beatrice Burton Neil Herring Gil Bub
author_sort	Jakub Tomek
title	COSMAS: a lightweight toolbox for cardiac optical mapping analysis
title_short	COSMAS: a lightweight toolbox for cardiac optical mapping analysis
title_full	COSMAS: a lightweight toolbox for cardiac optical mapping analysis
title_fullStr	COSMAS: a lightweight toolbox for cardiac optical mapping analysis
title_full_unstemmed	COSMAS: a lightweight toolbox for cardiac optical mapping analysis
title_sort	cosmas: a lightweight toolbox for cardiac optical mapping analysis
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/5de9830f1263460b9808cc02bb4fe0c6
work_keys_str_mv	AT jakubtomek cosmasalightweighttoolboxforcardiacopticalmappinganalysis AT zhinuojennywang cosmasalightweighttoolboxforcardiacopticalmappinganalysis AT rebeccaannbeatriceburton cosmasalightweighttoolboxforcardiacopticalmappinganalysis AT neilherring cosmasalightweighttoolboxforcardiacopticalmappinganalysis AT gilbub cosmasalightweighttoolboxforcardiacopticalmappinganalysis
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COSMAS: a lightweight toolbox for cardiac optical mapping analysis

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