IOCBIO Sparks detection and analysis software

Martin Laasmaa,Rikke Birkedal,Marko Vendelin,Niina Karro

doi:10.7717/peerj.6652

Abstract

Analysis of calcium sparks in cardiomyocytes can provide valuable information about functional changes of calcium handling in health and disease. As a part of the calcium sparks analysis, sparks detection and characterization is necessary. Here, we describe a new open-source platform for automatic calcium sparks detection from line scan confocal images. The developed software is tailored for detecting only calcium sparks, allowing us to design a graphical user interface specifically for this task. The software enables detecting sparks automatically as well as adding, removing, or adjusting regions of interest marking each spark. The results of the analysis are stored in an SQL database, allowing simple integration with statistical tools. We have analyzed the performance of the algorithm using a large set of synthetic images with varying spark sizes and noise levels and also compared the analysis results with results obtained by software established in the field. The use of our software is illustrated by an analysis of the effect of isoprenaline (ISO) on spark frequency, amplitude, and spatial and temporal characteristics. For that, cardiomyocytes from C57BL/6 mice were used. We demonstrated an increase in spark frequency, tendency of having larger spark amplitudes, sparks with a longer duration, and occurrence of multiple sparks from the same site in the presence of ISO. We also show that the duration and the width of sparks with the same amplitude were similar in the absence and presence of ISO. The software was released as an open source repository and is available for free use and collaborative development.

Highlights

IntroductionDuring cardiac excitation-contraction (EC) coupling, a rapid change in the cell’s membrane potential initiates a transient change in intracellular calcium concentration
During cardiac excitation-contraction (EC) coupling, a rapid change in the cell’s membrane potential initiates a transient change in intracellular calcium concentration. This change is mainly caused by the opening of L-type Ca2+ channels in the sarcolemma allowing Ca2+ to enter the cell, which in turn triggers Ca2+ release from the sarcoplasmic reticulum (SR) by the opening of ryanodine receptors (RyRs) in the SR (Bers, 2002)
Evaluation of the spark morphology estimation Using the same synthetic data as for evaluation of spark detection algorithm, we looked into estimated spark amplitude and its temporal (FDHM) and spatial (FWHM) characteristics

Summary

Introduction

During cardiac excitation-contraction (EC) coupling, a rapid change in the cell’s membrane potential initiates a transient change in intracellular calcium concentration. This change is mainly caused by the opening of L-type Ca2+ channels in the sarcolemma allowing Ca2+ to enter the cell, which in turn triggers Ca2+ release from the sarcoplasmic reticulum (SR) by the opening of ryanodine receptors (RyRs) in the SR (Bers, 2002). Ca2+ release from the RyRs can occur spontaneously in an unstimulated cell (Cheng & Lederer, 2008) These elementary Ca2+ release events in a cell can be visualized with a confocal microscope by recording changes in fluorescence of a Ca2+ sensitive dye (Ca2+ sparks), which occur as a brief, localized increase in the recorded signal.

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