Transparent organisms such as fish embryos are being increasingly used for environmental toxicology studies. These studies require estimating a number of physiological parameters. These estimations may be diverse in nature and can be a challenge to automate. Among these, an example is the development of reliable and repeatable automated assays for the determination of heart rates. To achieve this, most existing method rely on cyclical luminance variations, since as the heart fills and empties, it become respectively brighter and darker. However, sometimes direct measurement of the heart rate may be difficult, depending on the age of the embryo, its actual transparency, and its aspect under the microscope. It may be easier to seek an indirect measurement. In this article, we estimate the heart function parameters, such as heart frequency, either from measuring the heart motion or from blood flow in arteries. This measurement is more complex from the image analysis point of view, but it is more precise, more physically meaningful and easier to use in practice and to automate than measuring illumination changes. It may also be more informative. We illustrate on medaka embryos.