Abstract
We present Stytra, a flexible, open-source software package, written in Python and designed to cover all the general requirements involved in larval zebrafish behavioral experiments. It provides timed stimulus presentation, interfacing with external devices and simultaneous real-time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely-swimming and head-restrained preparations. Stytra logs all recorded quantities, metadata, and code version in standardized formats to allow full provenance tracking, from data acquisition through analysis to publication. The package is modular and expandable for different experimental protocols and setups. Current releases can be found at https://github.com/portugueslab/stytra. We also provide complete documentation with examples for extending the package to new stimuli and hardware, as well as a schema and parts list for behavioral setups. We showcase Stytra by reproducing previously published behavioral protocols in both head-restrained and freely-swimming larvae. We also demonstrate the use of the software in the context of a calcium imaging experiment, where it interfaces with other acquisition devices. Our aims are to enable more laboratories to easily implement behavioral experiments, as well as to provide a platform for sharing stimulus protocols that permits easy reproduction of experiments and straightforward validation. Finally, we demonstrate how Stytra can serve as a platform to design behavioral experiments involving tracking or visual stimulation with other animals and provide an example integration with the DeepLabCut neural network-based tracking method.
Highlights
The central goal of systems neuroscience is to explain the neural underpinnings of behavior
The same experimental paradigm has to be replicated in different experimental setups in order to combine it with different recording or stimulation techniques, and it needs to be reproducible across different laboratories
In addition to the open-source software, we are contributing to the nascent open hardware movement [4] and are providing a complete description of the hardware used for conducting behavioral experiments
Summary
The central goal of systems neuroscience is to explain the neural underpinnings of behavior. To investigate the link between sensory input, brain activity and animal behavior, relevant. Stytra: An open-source package for stimulation, tracking and behavioral experiments behavioral variables have to be recorded and quantified. The code used is based on expensive software packages (such as LabView or Matlab), with open-source options for hardware control generally limited to one particular type or brand of devices. The same experimental protocol has to be implemented many times, wasting time and increasing potential sources of error. This makes sharing the code for replicating a scientific finding under the same experimental conditions very difficult
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