1. BehaviorAnnotator: a Matlab program that facilitates the manual annotation of self-defined behaviors. The videos should be in .seq format acquired using Streampix (Norpix) or in .avi format. To use, download the toolbox from the below link: https://github.com/pdollar/toolbox; Add it to the Matlab path and type “behaviorAnnotator” in the command window. You will need to create a “config” file using Notebook that defines the behaviors to be annotated. Here is an example config file. The tool was generated by Piotr Dollar (Pietro Perona lab, Caltech) in collaboration with Dayu Lin (David Anderson lab, Caltech) and was first used in this paper.
2. SimBA: an automated social behavior recognition software created by Simon Nilsson (Sam A. Golden lab, UW) with contribution from Xiaoyu Tong (Dayu Lin lab, NYULMC). To download the software using the link: https://github.com/sgoldenlab/simba.
Related paper: Simple Behavioral Analysis (SimBA) – an open source toolkit for computer classification of complex social behaviors in experimental animals.
3. SLPtool.py: this python package assigns identities of two same-colored mice based on their unique features (e.g. head implant or not). The package was developed by Xiaoyu Tong (Dayu Lin lab, NYULMC). Download the package from the link: https://github.com/bd125/Lin_Lab_Sleap_extension. A detailed PowerPoint presentation can be found through the link that explains how to use the package.
Track 0: reliable predictions of implanted mouse
Track 1: reliable predictions of non-implanted mouse
Track 2: unreliable predictions of implanted mouse
Track 3: unreliable predictions of non-implanted mouse