bedsy 0.2b1

The BeDSy is a platform for hardware triggering and synchronisation of equipment for laboratory animal behavioural monitoring.

BeDSy - Behaviour-recording Device Synchroniser

What is it?

The BeDSy (Behaviour-recording Device Synchroniser) is a platform for hardware triggering and synchronisation of equipment for laboratory animal behavioural monitoring.

It consists of two components: this Python package, which interfaces with the BeDsyino, a hardware platform which sends custom trigger signals to animal behaviour-monitoring devices.

How to install?

BeDSy is available on PyPi can be installed with pip:

pip install bedsy

Dependencies

• pySerial - can be also be installed with pip

History

I (Davor Virag) developed the BeDSy platform with immense help from Paul Mieske and indispensible advice by Pia Kahnau during my stay with them at the German Federal Institute for Risk Assessment (BfR) in September 2023, where I was gracefully hosted by their brilliant PI, Lars Lewejohann, as part of my Short-Term Scientific Mission (STSM) funded by the COST action "Improving biomedical research by automated behaviour monitoring in the animal home-cage - TEATIME" (CA20135).

BeDSy was originally developed to improve video and audio synchronisation between several Basler cameras and the AviSoft UltraSoundGate for Paul's very cool upcoming research project.

Current state

This package is quite simple and seems to work fairly well. I don't have any major plans for it, except for adding sorely needed comments and documentation. It's currently been tested on Windows only, but I think it should work on Linux as well.

For an example (though not very clean) implementation into an existing project, see Basler GUI Updated, a continuation of Niek Andresen's Basler GUI Py project.

The BeDsyino is, however, still cooking. While the code is mostly complete, only a single hand-soldered, protoboard-based prototype has been developed thus far. A modular, extensible hardware platform is currently in the works. For more info, please check that repo.

How does it work

The module provides communication with BeDsyino, but requires the user to handle start/stop messages (i.e. it won't raise an exception if it doesn't receive a stop message after calling the stop_bedsy() method).

TO DO - expand

License

The code is distributed under GPLv3.