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

BMC Biology
Yoram Ben-Shaul

Abstract

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. 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. 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.

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Citations

Oct 16, 2019·Nature Methods·Claire N BedbrookFrances H Arnold
Jan 12, 2020·Nature Communications·Sungsoo KimWon Do Heo
Jan 30, 2020·Current Protocols in Neuroscience·Hadley C Bergstrom
May 17, 2017·BMC Biology·Winthrop F Gillis, Sandeep R Datta
Jun 23, 2019·Nature Protocols·Tanmay NathMackenzie Weygandt Mathis
Nov 24, 2019·Nature Communications·Guillaume EtterSylvain Williams
May 31, 2019·BMC Biology·Sandeep Robert Datta
Apr 9, 2020·Frontiers in Neuroscience·Annie LiuNathan N Urban
Jul 1, 2020·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Lukas von ZieglerJohannes Bohacek
Jul 28, 2020·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Oliver SturmanJohannes Bohacek
Sep 25, 2018·Frontiers in Behavioral Neuroscience·Elísabet Bello-ArroyoMaría Victoria Gómez-Gaviro
Aug 22, 2018·Nature Neuroscience·Alexander MathisMatthias Bethge
Oct 1, 2020·Journal of Neurophysiology·Rebecca Nicole LeesTudor Constantin Badea
Oct 20, 2019·Bio-protocol·Jay M PatelBenjamin R Arenkiel
Mar 5, 2021·Nature·Nao Horio, Stephen D Liberles
Jul 22, 2017·Journal of Neuroscience Methods·A GiovannucciD Masip
Oct 17, 2019··Jessica SwansonBenjamin Arenkiel

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Software Mentioned

VideoReader
OptiMouse
Windows
MATLAB GUIDE
Ethovision
ANT
Prepare
Github
Analysis
MATLAB

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