Integrative whole-brain neuroscience in larval zebrafish

Curr Opin Neurobiol. 2018 Jun;50:136-145. doi: 10.1016/j.conb.2018.02.004. Epub 2018 Mar 20.


Due to their small size and transparency, zebrafish larvae are amenable to a range of fluorescence microscopy techniques. With the development of sensitive genetically encoded calcium indicators, this has extended to the whole-brain imaging of neural activity with cellular resolution. This technique has been used to study brain-wide population dynamics accompanying sensory processing and sensorimotor transformations, and has spurred the development of innovative closed-loop behavioral paradigms in which stimulus-response relationships can be studied. More recently, microscopes have been developed that allow whole-brain calcium imaging in freely swimming and behaving larvae. In this review, we highlight the technologies underlying whole-brain functional imaging in zebrafish, provide examples of the sensory and motor processes that have been studied with this technique, and discuss the need to merge data from whole-brain functional imaging studies with neurochemical and anatomical information to develop holistic models of functional neural circuits.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • Animals, Genetically Modified
  • Brain* / diagnostic imaging
  • Brain* / growth & development
  • Brain* / metabolism
  • Calcium / metabolism
  • Larva*
  • Microscopy, Fluorescence
  • Neuroimaging
  • Neurosciences / methods*
  • Zebrafish


  • Calcium