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Background  Accurate determination of mouse positions from video data is crucial for various types of behavioral analyses. While detection of body positions is straightforward, the correct identification of nose positions, usually more informative, is far more challenging. The difficulty is largely due to variability in mouse postures across frames.    Results  Here, we present OptiMouse, an extensively documented open-source MATLAB program providing comprehensive semiautomatic analysis of mouse position data. The emphasis in OptiMouse is placed on minimizing errors in position detection. This is achieved by allowing application of multiple detection algorithms to each video, including custom user-defined algorithms, by selection of the optimal algorithm for each frame, and by correction when needed using interpolation or manual specification of positions.    Conclusions  At a basic level, OptiMouse is a simple and comprehensive solution for analysis of position data. At an advanced level, it provides an open-source and expandable environment for a detailed analysis of mouse position data.    Electronic supplementary material  The online version of this article (doi:10.1186/s12915-017-0377-3) contains supplementary material, which is available to authorized users.

OptiMouse: a comprehensive open source program for reliable detection and analysis of mouse body and nose positions