Zebrafish are often used as a model organism for in vivo brain imaging, because they are transparent. Or at least that is what many people think who do not work with zebrafish. In reality, most people use zebrafish larvae for in vivo imaging, typically not older than 5 days (post fertilization). At this developmental stage, the total larval body length is still less than the brain size of the adult fish. After 3-4 weeks, the fish look less like tadpoles and more like fish, measuring 10-15 mm in size (see also video below). They attain the full body length of approx. 25 to 45 mm within 3-4 months.

This video shows a zebrafish larva (7 days old), two adult zebrafish (16 months old) and a juvenile zebrafish (4.5 weeks old).

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After 4-5 days, the brain size of larvae exceeds the dimensions that can be imaged with cellular resolution in vivo using light sheet or confocal microscopy when embedded in agarose. After approx. 4 weeks, even for unpigmented fish the thickened skull makes imaging of deeper brain regions very difficult. Superficial brain regions like the tectum are better accessible, but fish of this age are too strong to be restrained by agarose embedding. Brain imaging for adult fish is still possible in ex vivo whole brain preparations [1], but with loss of behavioral readout. Use of toxins for immobilization is an option (e.g. with curare in zebrafish [2] or in other fish species [3]), but not a legal one in some countries, including Switzerland. These are some of the reasons why most people stick to the simple zebrafish larva. My PhD lab is one of the few that does physiology in adult zebrafish.