fish-simulator-test 0.0.2

Simulate zebrafish swim from tail angle tracking data

Zebrafish Tail Animator

Python toolbox to transform zebrafish tracking data to tail animations

Description

zf_animator is a Python package used to create visualisation of how swimming data looks from high-speed tracking data. The typical data used should be the tail angle along segments of the tail. The package will convert these tail angles to x- y- coordinates, and interpolate many more points along the range of tracked tail segments. These sets of coordinates will then transform slices of the zebrafish image, producing a stack of .png files that can be rendered into an mp4 file.

Installation

To convert the .png files to an .mp4 animation requires ffmpeg to be installed on the running computer. This can be install in Ubuntu in the terminal:

sudo apt install ffmpeg

Or with OS X can be installed:

brew install ffmpeg

Check it is installed by running which ffmpeg in the terminal. More details can be found here.

Dependencies

Default zebrafish image

Ref the source of the image

Example

Key Functions