mousecam

(click here for a html version)

3D models and data extraction/analysis code for the head-mounted camera system described in:

AF Meyer, J Poort, J O'Keefe, M Sahani, and JF Linden: A head-mounted camera system integrates detailed behavioral monitoring with multichannel electrophysiology in freely moving mice, Neuron, Volume 100, p46-60, 2018. link (open access)

This repository contains the following:

mousecam: a Python package with functions for extracting and analyzing data recorded using the camera system, including
- pupil fitting (including GUI)
- body tracking (including GUI)
- image registration (via fiji/imagej)
- extraction of head orientation
parts: 3D models (openscad/stl) and building instructions for the head-mounted camera system

News

08/06/2020: Paper on head and eye movements in freely moving mice published in Current Biology
20/02/2020: New preprint using the mousecam on bioRxiv
21/11/2018: Add design files for new camera module
04/11/18: This page is now also organized in a website format.
07/11/18: Added websites with step-by-step building instructions
28/11/18: The project is now on open-ephys.org
12/01/19: Added intructions on how to remove IR filter from camera module
14/02/19: Mousecam featured on openbehavior.com

Step-by-step building instructions

1. Parts list

2. Building instructions

3. Implantation

4. Calibration

Software

Head-mounted camera code

Custom camera software for the Raspberry Pi (RPi), which also integrates with the open-ephys plugin-GUI. As this software uses zeromq (with bindings for many programming languages) for communication between the recording computer and the RPi, it can easily be extended/adapted to other systems.

Measurement of head orientation/movement data

Code (including open-ephys plugin) for reading data from intertia measurement unit (IMU) sensors and synchronizing movement data with neural recordings is available here.

Behavioral segmentation

A Python package for behavioral scoring (including GUI for manual annotation) can be found here.

Contribute

If you are looking for a different variant of the design or want to contribute modified and/or new designs, you can find all files in the 3D model directory. Please use the issue tracker to report problems with building the camera system and create pull requests for improved/new designs.

Issue Tracker: https://github.com/arnefmeyer/mousecam/issues
Source Code: https://github.com/arnefmeyer/mousecam
Project Website: https://arnefmeyer.github.io/mousecam

References

@Article{Meyer2018,
  author    = {Meyer, Arne F. and Poort, Jasper and O’Keefe, John and Sahani, Maneesh and Linden, Jennifer F.},
  title     = {A Head-Mounted Camera System Integrates Detailed Behavioral Monitoring with Multichannel Electrophysiology in Freely Moving Mice},
  journal   = {Neuron},
  year      = {2018},
  volume    = {100},
  number    = {1},
  month     = oct,
  pages     = {46--60},
  issn      = {0896-6273},
  doi       = {10.1016/j.neuron.2018.09.020},
  url       = {https://doi.org/10.1016/j.neuron.2018.09.020},
  publisher = {Elsevier},
}

@Article{Meyer2020,
  author    = {Meyer, Arne F. and O'Keefe, John and Poort, Jasper},
  title     = {Two Distinct Types of Eye-Head Coupling in Freely Moving Mice},
  doi       = {10.1016/j.cub.2020.04.042},
  issn      = {0960-9822},
  number    = {11},
  pages     = {2116--2130},
  url       = {https://doi.org/10.1016/j.cub.2020.04.042},
  volume    = {30},
  comment   = {doi: 10.1016/j.cub.2020.04.042},
  journal   = {Current Biology},
  month     = jun,
  publisher = {Elsevier},
  year      = {2020},
}

der-tim / mousecam