Automatic and Robust Estimation of Heart Rate in Zebrafish Larvae

Noncontact assessment of heart rate (HR) in Zebrafish larvae, based on a video record of the organism, acquired using a camera mounted on a microscope, has gained enormous significance. Completely automatic and robust estimation of HR from videos of nontransgenic larvae requires the determination of an appropriate region of interest (ROI), followed by suitable signal processing steps. Toward such a goal, we develop a fully automatic and adaptive ROI enclosing a predominant portion of the beating heart, irrespective of the image resolution and zoom. The information within the ROI is used to get one or more time series, to be processed for extracting the signal containing information about the beating heart. Among the various possibilities, we show that the multichannel approach exploiting color information and based on independent component analysis to extract the cardiac signal--is desirable, due to several reasons, including its ability to handle noise, minor movements of the larvae or of the platform, and statistical performance. The proposed sequence of algorithms is validated on videos of 41 larvae (2 days and 4 days postfertilization). The computer estimated values of HR compared well with the ground truth obtained by visual-counting. We have also devised a method of tracking the ROI associated with drifting larvae and tested it on real data. In addition, an example of handling a type of arrhythmia is given.