I am trying to use heart beat as a developmental index to study the effect of environmental contaminants. I will be using MS-222 (Tricaine methanesulfonate) to anesthetize the larvae.
Ms-222 will definitely affect the heart beat. In general to measure it you should take a short video of the heart and measure the image change over time. I recommend this publications.
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Ultrasound (like by the company of Fujifilm - Visualsonics) may be an option to measure the heartbeat. There are devices available for adults, they can probably also used in larvae. But Tricain (MS-222) is affecting the heartbeat, like probably all anesthetics. Depending on size and age of the larvae it may work with just embedding them into soft agarose to immobilize them. Or use a wet sponge with a slit in it to position the larvae.
You can use methyl cellulose for mounting the live zebrafish larvae under microscope. Record the video and data can be analysed using many softwares like danioscope