sisyphy

Minimal code for handling data acquisition and position extraction from the spherical treadmill VR system described in Shapcott et al, 2022 (here 3D printing files & hardware instructions).

This package is a Python-based alternative to the original Unreal Engine system. Although Python-based, it offers a set of tools to stream the data via ZeroMQ or tcp protocols, to interface it with custom applications (e.g. with MATLAB, using ViRMEn, or Bonsai-RX).

The project is very much under development at the moment. Although the core components are mature and will probably be stable, there's still a lot to polish in the specifics of interfaces. It is still very open to suggestions, so feedbacks are welcome!

Package organization

hardware_readers

This module contains the interface to the hardware - the spherical threadmill and the mice that read it.

The core classes from here are:

• RawUsbSphereReaderProcess: process that reads raw speeds from the sphere mice and streams them in a queue.
• CalibratedSphereReaderProcess: process that streams calibrated data in the queue.

streamers

The core abstract interface class of the package is MouseStreamer. It implements a process that runs and streams mouse velocities. Subclasses implement specific streamers:

• TCPMouseStreamer: stream mouse data using TCP protocol.
• ZMQMouseStreamer: stream mouse data using ZMQ.

mat

The mat folder contains a MATLAB code snippet that can be used to read the TCP streamed velocities in MATLAB, to use them to control a virtual environment with the VIRmEm software.

Time synchronization [deprecated, old!]

This package also include code for synching the acquisition with Arduino-generated barcodes using the system described here from the Optogenetics and Neural Engineering (ONE) Core at the University of Colorado School of Medicine.

In the future this code might be moved to an independent package.

Hardware configuration

Mouse reading

Detailled instructions on the hardware configuration can be found in the original setup description. In brief, to make the mouse readable in Python:

1. figure out vendor and device id. The following could help, knowing ie the Logitech vendor id (0x046d):

import usb1
iGIdVendor = 0x046d  # Logitech id
ctx = usb1.LibUSBContext()
alldevs = ctx.getDeviceList()
print([dev for dev in alldevs if dev.getVendorID()==iGIdVendor])  # list ids of Logitech devices

2. Replace the device drivers with standard WinUSB. This was done using the intuitive Zadig interface. From the website there are extensive tutorials reachable.

3. At this point, with the little script readmouse.py we can read mouse motion! As a nice side effect, replacing the mouse drivers stops the normal functioning of the mouse for the OS.

Note: This was done and tested with LogiTech502 mouse, and works specifically with a pair of mice of that model!

Run sisyphy

With Bonsai

For streaming to Bonsai, we will be using ZMQ communication. You will have to run sisyphy.streamers.zmq_streamer.py