Jupyter Notebooks for analysis

We are constantly developing new tools to analyze the trajectories that outputs. We provide Jupyter Notebooks with examples of analysis routines for groups of animals.

The trajectorytools python module

You can install the trajectorytools module from the following GitHub repository:

Jupyter Notebooks

You can find some analysis routines from 1 implemented with the trajectorytools module in the Jupyter Lab Notebook trajcetoroies.ipynb in the following GitLab repository:

Figures generated from our Jupyter Notebooks for a video of 10 juvenile fish

Smoothed trajectories


Velocities and accelerations


Density of neighbours around a focal fish


Polar distributions of positions, turnings and accelerations


Inter-individual distance histograms compared with shuffled trajectories


Hinz, R. C., & de Polavieja, G. G. (2017). Ontogeny of collective behavior reveals a simple attraction rule. Proceedings of the National Academy of Sciences