A passive, camera-based head-tracking system for real-time, 3D estimate of head position and orientation in rodents

Vanzella, Walter; Grion, Natalia; Bertolini, Daniele; Perissinotto, Andrea; Zoccolan, Davide

doi:10.1101/599365

Cited by 2 publications

(2 citation statements)

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“…This has the advantage that it simplifies the tracking problem. However, it would also be useful to extend the approach to freely moving animals, perhaps by combining whisker tracking with head-body tracking [33][34][35][36][37][38][39][40][41].…”

Section: Discussionmentioning

confidence: 99%

A system for tracking whisker kinematics and whisker shape in three dimensions

et al. 2020

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Quantification of behaviour is essential for biology. Since the whisker system is a popular model, it is important to have methods for measuring whisker movements from behaving animals. Here, we developed a high-speed imaging system that measures whisker movements simultaneously from two vantage points. We developed a whisker tracker algorithm that automatically reconstructs 3D whisker information directly from the 'stereo' video data. The tracker is controlled via a Graphical User Interface that also allows user-friendly curation. The algorithm tracks whiskers, by fitting a 3D Bezier curve to the basal section of each target whisker. By using prior knowledge of natural whisker motion and natural whisker shape to constrain the fits and by minimising the number of fitted parameters, the algorithm is able to track multiple whiskers in parallel with low error rate. We used the output of the tracker to produce a 3D description of each tracked whisker, including its 3D orientation and 3D shape, as well as bending-related mechanical force. In conclusion, we present a noninvasive, automatic system to track whiskers in 3D from high-speed video, creating the opportunity for comprehensive 3D analysis of sensorimotor behaviour and its neural basis.

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Section: Discussionmentioning

confidence: 99%

A system for tracking whisker kinematics and whisker shape in three dimensions

et al. 2020

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Section: Discussionmentioning

confidence: 99%

A system for tracking whisker kinematics and whisker shape in three dimensions

Petersen

Rodriguez

Evans

et al. 2019

Preprint

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25Quantification of behaviour is essential for systems neuroscience. Since the whisker system is a major model system for 26 investigating the neural basis of behaviour, it is important to have methods for measuring whisker movements from 27 behaving animals. Here, we developed a high-speed imaging system that measures whisker movements simultaneously 28 from two vantage points. We developed an algorithm that uses the 'stereo' video data to track multiple whiskers by 29 fitting 3D curves to the basal section of each target whisker. By using temporal information to constrain the fits, the 30 algorithm is able to track multiple whiskers in parallel with low error rate. We used the output of the tracker to produce a 31 3D description of each tracked whisker, including its 3D orientation and 3D shape, as well as bending-related mechanical 32 force. In conclusion, we present an automatic system to track whiskers in 3D from high-speed video, creating the 33 opportunity for comprehensive 3D analysis of sensorimotor behaviour and its neural basis. 34 Author summary 35The great ethologist Niko Tinbergen described a crucial challenge in biology to measure the "total movements made by 36 the intact animal". Advances in high-speed video and machine analysis of such data have made it possible to make 37 profound advances. Here, we target the whisker system. The whisker system is a major experimental model in 38 neurobiology and, since the whiskers are readily imageable, the system is ideally suited to machine vision. Rats and mice 39 explore their environment by sweeping their whiskers to and fro. It is important to measure whisker movements in 3D, 40 since whiskers move in 3D and since the mechanical forces that act on them are 3D. However, the problem of 41 automatically tracking whiskers in 3D from video has generally been regarded as prohibitively difficult. Our innovation 42 here is to extract 3D information about whiskers using a two-camera, high-speed imaging system and to develop 43 computational methods to infer 3D whisker state from the imaging data. Our hope is that this study will facilitate 44 comprehensive, 3D analysis of whisker behaviour and, more generally, contribute new insight into brain mechanisms of 45 perception and behaviour. 46 47 48 50 Substantial progress towards the long-standing ambition of measuring "total movements made by the intact animal" (1) is 51 coming from the application of powerful machine vision methods to video recordings of behaving animals (2). Since the 52 whisker system is a major experimental model in neuroscience and since the whiskers are readily imageable (3,4), the 53 whisker system is ideally suited to this endeavour. Tracking the whiskers of mice/rats has already deepened our 54 understanding of active sensation and refined our capacity to relate behaviour to neural mechanisms (5-10) Our aim here 55 was to develop a method to track whisker movements and whisker shape in 3D in behaving mice at millisecond temporal 56 resolution. 57Whisker movement is 3D. During each whisking...

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A passive, camera-based head-tracking system for real-time, 3D estimate of head position and orientation in rodents

Cited by 2 publications

References 78 publications

A system for tracking whisker kinematics and whisker shape in three dimensions

A system for tracking whisker kinematics and whisker shape in three dimensions

A system for tracking whisker kinematics and whisker shape in three dimensions

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