motr documentation

motr is a single-camera, video-based, flexible tracking system for mice, which can track many, socially-housed mice for days, or a single mouse for a few minutes. You can use the online manual (below) or you can download the manual as a single PDF.

Getting started

Which motr should I use?
Downloading and installing motr

Recording Video

Picking a camera and recording method
Preparing the mice
Preparing the recording arena
Recording multi-mouse video
Recording single mouse video for identity templates

Running motr

Training the identity template
Tracking the mice

Looking at the results

Data files
Track file format

Running motr on a cluster


List of useful materials
Hysterically brief git primer
Output directory structure


motr was developed by Shay Ohayon, Adam Taylor, Ofer Avni, Roian Egnor, and Pietro Perona, with help from Josh Neunuebel, Kelly Seagraves, Kristin Branson and Billy Rowell.