Data analysis

While idtracker.ai’s job ends when the trajectory files are validated. There are some extra tools (not part of but compatible with idtracker.ai), Trajectorytools and Fish Midline.

Trajectorytools

A Python package that performs basic trajectory analysis and it is available at polavieja_lab/trajectorytools.

You can find some analysis routines from [1] implemented with trajectorytools in polavieja_lab/idtrackerai_notebooks. Here we present some of the analysis we get using a 10 juvenile fish video:

Smoothed trajectories (left) and density of neighbors around a focal fish (right)

Velocities and accelerations

Polar distributions of positions, turnings and accelerations

Inter-individual distance histograms compared with shuffled trajectories

Fish Midline

A short Python script available at polavieja_lab/midline to extract posture information of animals tracked with idtracker.ai. Intended to be used with fish data but easily customizable and adaptable.

Example of posture information extracted with Fish Midline.

References

[1]

Hinz, R. C., & de Polavieja, G. G. (2017). Ontogeny of collective behavior reveals a simple attraction rule. Proceedings of the National Academy of Sciences, 114(9), 2295-2300.