An automatic method to calculate heart rate from zebrafish larval cardiac videos

Abstract

BackgroundZebrafish is a widely used model organism for studying heart development and cardiac-related pathogenesis. With the ability of surviving without a functional circulation at larval stages, strong genetic similarity between zebrafish and mammals, prolific reproduction and optically transparent embryos, zebrafish is powerful in modeling mammalian cardiac physiology and pathology as well as in large-scale high throughput screening. However, an economical and convenient tool for rapid evaluation of fish cardiac function is still in need. There have been several image analysis methods to assess cardiac functions in zebrafish embryos/larvae, but they are still improvable to reduce manual intervention in the entire process. This work developed a fully automatic method to calculate heart rate, an important parameter to analyze cardiac function, from videos. It contains several filters to identify the heart region, to reduce video noise and to calculate heart rates.ResultsThe proposed method was evaluated with 32 zebrafish larval cardiac videos that were recording at three-day post-fertilization. The heart rate measured by the proposed method was comparable to that determined by manual counting. The experimental results show that the proposed method does not lose accuracy while largely reducing the labor cost and uncertainty of manual counting.ConclusionsWith the proposed method, researchers do not have to manually select a region of interest before analyzing videos. Moreover, filters designed to reduce video noise can alleviate background fluctuations during the video recording stage (e.g. shifting), which makes recorders generate usable videos easily and therefore reduce manual efforts while recording.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2166-6) contains supplementary material, which is available to authorized users.

An Overview of Methods for Cardiac Rhythm Detection in Zebrafish

“…However, using electrocardiographic signals in a zebrafish embryo requires precise positioning of the electrodes to obtain reproducible signals [ 18 ]. Kang et al found outthat counting heartbeats manually was more unreliable as there is a high possibility of biased results due to individual error, which measures the variation between repeated experiments by an individual, and from the crowd error, which measures the variation between different operators, even when the counting was done by trained individuals [ 19 ]. Gaur et al [ 20 ] also reported the manual counting method.…”

Reduced metabolic rate and increased heart beat as early signs of sub lethal Copper toxicity in developing Zebrafish

“…The heartbeat rate can be an early sign and a reliable indicator in assessing the severity of Cu toxicity for developing zebrafish with minimal laboratory equipment and resources. This protocol may be easily strengthened by specialised image analysis software for automatic zebrafish heartbeat detection and analysis (Pylatiuk et al, 2014;Kang et al, 2018), reducing time and resources for initial evaluation of Cu toxicity on developing zebrafish. It would be interesting to validate this method in other fish species or environmental pollutants for potential reduction of required resources and experimental animals in pilot experiments for toxicological research.…”

“…The use of a range of anatomical, biochemical, and viability indicators are useful in assessing the toxic effect of enhanced concentrations of Cu on developing embryos (Parichy et al, 2009). Heartbeat rate is one of the parameters affected by heavy metals and has the potential to be widely and easily used for toxicological research on developing zebrafish embryos (Kang et al, 2018). It is a reliable method for piloting experimental work required for designing toxicological experiments, such as selecting a potentially toxic agent and its concentration for further research.…”

Adult and Developing Zebrafish as Suitable Models for Cardiac Electrophysiology and Pathology in Research and Industry

“…Different platforms and software, such as ZebraPace (Zebrafish Precise Algorithm for Cardiac-rhythm Estimation), MicroZebraLab TM (v3.5, ViewPoint, Lyon, France) or DanioVison system (Noldus Information Technology, Netherlands), have been developed to quantify the contractility, heart rate, incidence of arrhythmia, and blood flow in zebrafish embryos/larvae (Parker et al, 2014;Gaur et al, 2018;Kang et al, 2018;Wang et al, 2020).…”