Abstract
IntelliCage is an automated system for recording the behavior of a group of mice housed together. It produces rich, detailed behavioral data calling for new methods and software for their analysis. Here we present PyMICE, a free and open-source library for analysis of IntelliCage data in the Python programming language. We describe the design and demonstrate the use of the library through a series of examples. PyMICE provides easy and intuitive access to IntelliCage data, and thus facilitates the possibility of using numerous other Python scientific libraries to form a complete data analysis workflow.
Highlights
In recent years, a number of automated environments for behavioral testing have been developed, based on RFID (Dell’omo, Shore, & Lipp, 1998; Galsworthy et al, 2005; Daan et al, 2011; Puscian et al, 2016) or video tracking of animals (de Chaumont et al, 2012; Weissbrod et al, 2013; Shemesh et al, 2013; Pérez-Escudero, Vicente-Page, Hinz, Arganda, & de Polavieja, 2014)
A number of automated environments for behavioral testing have been developed, based on RFID (Dell’omo, Shore, & Lipp, 1998; Galsworthy et al, 2005; Daan et al, 2011; Puscian et al, 2016) or video tracking of animals. Such automated systems have many advantages compared to the traditional behavioral tests, such as the reduction of the animal stress caused by isolation and handling (Heinrichs & Koob, 2006; Sorge et al, 2014), the possibility of studying social interactions in group-housed animals (Kiryk et al, 2011), the possibility of long-term studies, and easier standardization of protocols in turn leading to better reproducibility of results between laboratories (Crabbe, Wahlsten, & Dudek, 1999; Chesler, Wilson, Lariviere, Rodriguez-Zas, & Mogil, 2002; Krackow et al, 2010; Codita et al, 2012; Morrison, 2014; Vannoni et al, 2014)
We present the analysis in more detail, including the estimation of how the mice performance in the discrimination task changed over time
Summary
A number of automated environments for behavioral testing have been developed, based on RFID (Dell’omo, Shore, & Lipp, 1998; Galsworthy et al, 2005; Daan et al, 2011; Puscian et al, 2016) or video tracking of animals (de Chaumont et al, 2012; Weissbrod et al, 2013; Shemesh et al, 2013; Pérez-Escudero, Vicente-Page, Hinz, Arganda, & de Polavieja, 2014). PyMICE is a free and open-source library that makes it easier to access and analyze IntelliCage data in the Python programming language. In Example 1 we show how to find numbers of visits of a specific mouse in which the first nosepoke was performed to either the left side or the right side of the corner.
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