CardIAP: calcium transients confocal image analysis tool

Ana Julia Velez Rueda; Luis Alberto Gonano; Agustín García Smith; Gustavo Parisi; María Silvina Fornasari; Leandro Matías Sommese

doi:10.3389/fbinf.2023.1137815

CardIAP: calcium transients confocal image analysis tool

Front Bioinform. 2023 Jul 14:3:1137815. doi: 10.3389/fbinf.2023.1137815. eCollection 2023.

Authors

Ana Julia Velez Rueda¹, Luis Alberto Gonano², Agustín García Smith¹, Gustavo Parisi¹, María Silvina Fornasari¹, Leandro Matías Sommese¹

Affiliations

¹ Departamento de Ciencia y Tecnología, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina.
² Centro de Investigaciones Cardiovasculares, Facultad de Medicina, CONICET, Universidad Nacional de La Plata, La Plata, Argentina.

Abstract

One of the main topics of cardiovascular research is the study of calcium (Ca2+) handling, as even small changes in Ca2+ concentration can alter cell functionality (Bers, Annu Rev Physiol, 2014, 76, 107-127). Ionic calcium (Ca2+) plays the role of a second messenger in eukaryotic cells, associated with cellular functions such as cell cycle regulation, transport, motility, gene expression, and regulation. The use of fluorometric techniques in isolated cells loaded with Ca2+-sensitive fluorescent probes allows quantitative measurement of dynamic events occurring in living, functioning cells. The Cardiomyocytes Images Analyzer Python (CardIAP) application addresses the need to analyze and retrieve information from confocal microscopy images systematically, accurately, and rapidly. Here we present CardIAP, an open-source tool developed entirely in Python, freely available and useable in an interactive web application. In addition, CardIAP can be used as a standalone Python library and freely installed via PIP, making it easy to integrate into biomedical imaging pipelines. The images that can be generated in the study of the heart have the particularity of requiring both spatial and temporal analysis. CardIAP aims to open the field of cardiomyocytes and intact hearts image processing. The improvement in the extraction of information from the images will allow optimizing the usage of resources and animals. With CardIAP, users can run the analysis to both, the complete image, and portions of it in an easy way, and replicate it on a series of images. This analysis provides users with information on the spatial and temporal changes in calcium releases and characterizes them. The web application also allows users to extract calcium dynamics data in downloadable tables, simplifying the calculation of alternation and discordance indices and their classification. CardIAP aims to provide a tool that could assist biomedical researchers in studying the underlying mechanisms of anomalous calcium release phenomena.

Keywords: alternans; calcium transient; confocal microscopy; discordance analysis; impaired calcium handling.

Grants and funding

This work was supported by the Universidad Nacional de Quilmes (PUNQ 2282/22) and the Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación, Argentina (PICT 0990/20). The funders had no influence on the study design, data collection, analysis, decision to publish, or preparation of the manuscript. LS, LG, GP, and MF are Consejo Nacional de Investigaciones Ciencia y Tecnología (CONICET) researchers. AV is a CONICET postdoctoral fellow.