Spiky: An ImageJ Plugin for Data Analysis of Functional Cardiac and Cardiomyocyte Studies

Abstract

Introduction and objective: Nowadays, investigations of heart physiology and pathophysiology rely more and more upon image analysis, whether for the detection and characterization of events in single cells or for the mapping of events and their characteristics across an entire tissue. These investigations require extensive skills in image analysis and/or expensive software, and their reproducibility may be a concern. Our objective was to build a robust, reliable and open-source software tool to quantify excitation–contraction related experimental data at multiple scales, from single isolated cells to the whole heart. Methods and results: A free and open-source ImageJ plugin, Spiky, was developed to detect and analyze peaks in experimental data streams. It allows rapid and easy analysis of action potentials, intracellular calcium transient and contraction data from cardiac research experiments. As shown in the provided examples, both classical bi-dimensional data (XT signals) and video data obtained from confocal microscopy and optical mapping experiments (XYT signals) can be analyzed. Spiky was written in ImageJ Macro Language and JAVA, and works under Windows, Mac and Linux operating systems. Conclusion: Spiky provides a complete working interface to process and analyze cardiac physiology research data.

Novel 2D/3D Hybrid Organoid System for High-Throughput Drug Screening in iPSC Cardiomyocytes

“…To assess calcium transients, we utilized an Image J plugin called Spiky, which is a software tool that quantifies excitation–contraction related experimental data, including intracellular calcium transients. 59 It detects peaks in the input by characterizing the temporal shift from baseline of a signal in an image, and then computes a variety of parameters for each peak, such as amplitude, time to peak, time between peaks, peak width, maximum slope of peak, and area under the curve. Spiky was run for each individual ROI.…”

Novel 2D/3D Hybrid Organoid System for High-Throughput Drug Screening in iPSC Cardiomyocytes

“…To assess calcium transients, we utilized an Image J plugin called Spiky, which is a software tool that quanti es excitation-contraction related experimental data, including intracellular calcium transients. 59 It detects peaks in the input by characterizing the temporal shift from baseline of a signal in an image, and then computes a variety of parameters for each peak, such as amplitude, time to peak, time between peaks, peak width, maximum slope of peak, and area under the curve. Spiky was run for each individual ROI.…”

KairoSight-3.0: A Validated Optical Mapping Software to Characterize Cardiac Electrophysiology, Excitation-Contraction Coupling, and Alternans

“…Since optical mapping studies require a fast rate of acquisition and fluorescent signals have a small fractional change, the acquired images often require post-processing to improve the signal-to-noise ratio (SNR) quality 5,9,10 . Accordingly, the analysis and interpretation of optical mapping data is both time-and resource-intensive, which has prompted the development of several unique software packages for semi-automated image processing and analysis (e.g., Rhythm 11 , ElectroMap 12 , ORCA 13 , COSMAS 14 , Spiky 15 ). A common feature across these software packages is the ability to generate epicardial action potential (AP) activation and repolarization maps.…”