Observing, analysing, modelling, and even changing the behaviour of zebrafish

  • Yushi Yang

Student thesis: Doctoral ThesisDoctor of Philosophy (PhD)


A group of animals is a typical active matter system, whose behaviour can be understood from the perspective of statistical physics.

Here we studied the behaviour of zebrafish experimentally. We developed a novel algorithm to extract fish locations from 2D images. By incorporating images captured from synchronised cameras, we calculated the 3D locations of individual fish in a group. The data-processing pipeline developed in this work allows the trajectories of the fish being recovered from the coordinates. We then analysed the collective behaviour of the zebrafish by different correlation functions. We find the macroscopic states of the fish can switch between ordered and disordered. The changing states of the fish is dominated by a dynamical length scale as well as a structural length scale. More specifically, the polarisation of fifty zebrafish correlate robustly with a dimensionless number, the ratio between the persistence length and the nearest neighbour distance of individual fish.

To understand the observed zebrafish behaviour, we proposed different models to fit the density distribution of the fish as well as the dynamics of the fish. For the spatial distribution of the fish, our model highlights the fish-environment interaction, that dominates the behaviour of small groups (N < 5), and the fish-fish interaction, that dominates the behaviour of large groups (N = 50). For the dynamics of the fish, our model revealed the importance of the orientational inertia for the fish individuals, and the alignment interaction between the fish.

Finally, we applied the established methods to biology, and studied the behavioural feature of the col11a2 mutant zebrafish, whose genetic modification is related to human diseases. The col11a2 mutant zebrafish individuals exhibited slower re-orientation, corresponding to a higher activity. Consequently, a group of col11a2 mutant zebrafish exhibited more ordered behaviour, compared to the wildtype zebrafish. The linkage between the individual behaviour and the collective behaviour of the col11a2 mutant zebrafish can be explained by our proposed active matter model.
Date of Award21 Jun 2022
Original languageEnglish
Awarding Institution
  • University of Bristol
SupervisorChrissy L Hammond (Supervisor) & Thomas J Machon (Supervisor)

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