Computational, Systems and Developmental Neuroscience

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Neural coding in the zebrafish brain

What is the `neural code' by which patterns of electrical activity in the brain represent information, how does this subserve behavior, and how do neural coding and behavior develop? We are investigating these questions using the zebrafish model system. Zebrafish larvae show sophisticated hunting behaviours from an early age. Furthermore they are transparent, so that we can use genetically-encoded calcium indicators to optically record the activity of many neurons simultaneously. By making experimental measurements of neural activity and hunting behaviour, and analysing these with a variety of sophisticated mathematical approaches, allows us to investigate how neural coding and complex behaviours develop in tandem during early life.

  • Spontaneous and evoked activity patterns diverge over development. In this paper in eLife we recorded spontaneous and evoked neural activity in the larval zebrafish tectum from 4 to 15 days post-fertilisation and found that, according to several metrics, spontaneous and evoked activitydiverged over development. This is different from the case in some other systems, and suggests that spontaneous activity in the developing tectum may not acting as a Bayesian prior for evoked activity.
  • Behavioral signatures of a developing neural code. How do neural codes critical for behavior emerge during development? In this paper in Current Biology we showed that during early life visually-driven hunting in larval zebrafish improves, and this is accompanied by increasing mutual information and improved decoding of visual stimuli in the optic tectum. Moreover, decoding can predict individual differences in hunting. See also this review paper in Trends in Neurosciences.
  • The development of spontaneous activity in the zebrafish brain. The optic tectum in the brain of the larval zebrafish is highly active even without visual input. In this paper in Current Biology we looked at this activity every day from 4-9 dpf (days post-fertilization) to examine how this activity develops. Using tools from graph theory we showed how the functional connectivity of the tectum changes over this time. By manipulations like raising fish in the dark we also showed that these changes were dependent on visual input during development. See also this review paper.
  • Limitations of neural map topography for decoding spatial information. A very common feature of brain wiring is that neighboring points on a sensory surface (eg, the retina) are connected to neighboring points in the brain. It is often assumed that this “topography” of wiring is essential for decoding sensory stimuli. However, in this paper in the Journal of Neuroscience we showed in the developing zebrafish that topographic decoding performs very poorly compared with methods that do not rely on topography. This suggests that, although wiring topography could provide a starting point for decoding at a very early stage in development, it may be replaced by more accurate methods as the animal gains experience of the world.