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A Markerless Pose Estimator Applicable to Limbless Animals

The analysis of kinematics, locomotion, and spatial tasks relies on the accurate detection of animal positions and pose. Pose and position can be assessed with video analysis programs, the “trackers.” Most available trackers represent animals as single points in space (no pose information available)...

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Autores principales: Garg, Vranda, André, Selina, Giraldo, Diego, Heyer, Luisa, Göpfert, Martin C., Dosch, Roland, Geurten, Bart R. H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8997243/
https://www.ncbi.nlm.nih.gov/pubmed/35418841
http://dx.doi.org/10.3389/fnbeh.2022.819146
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author Garg, Vranda
André, Selina
Giraldo, Diego
Heyer, Luisa
Göpfert, Martin C.
Dosch, Roland
Geurten, Bart R. H.
author_facet Garg, Vranda
André, Selina
Giraldo, Diego
Heyer, Luisa
Göpfert, Martin C.
Dosch, Roland
Geurten, Bart R. H.
author_sort Garg, Vranda
collection PubMed
description The analysis of kinematics, locomotion, and spatial tasks relies on the accurate detection of animal positions and pose. Pose and position can be assessed with video analysis programs, the “trackers.” Most available trackers represent animals as single points in space (no pose information available) or use markers to build a skeletal representation of pose. Markers are either physical objects attached to the body (white balls, stickers, or paint) or they are defined in silico using recognizable body structures (e.g., joints, limbs, color patterns). Physical markers often cannot be used if the animals are small, lack prominent body structures on which the markers can be placed, or live in environments such as aquatic ones that might detach the marker. Here, we introduce a marker-free pose-estimator (LACE Limbless Animal traCkEr) that builds the pose of the animal de novo from its contour. LACE detects the contour of the animal and derives the body mid-line, building a pseudo-skeleton by defining vertices and edges. By applying LACE to analyse the pose of larval Drosophila melanogaster and adult zebrafish, we illustrate that LACE allows to quantify, for example, genetic alterations of peristaltic movements and gender-specific locomotion patterns that are associated with different body shapes. As illustrated by these examples, LACE provides a versatile method for assessing position, pose and movement patterns, even in animals without limbs.
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spelling pubmed-89972432022-04-12 A Markerless Pose Estimator Applicable to Limbless Animals Garg, Vranda André, Selina Giraldo, Diego Heyer, Luisa Göpfert, Martin C. Dosch, Roland Geurten, Bart R. H. Front Behav Neurosci Behavioral Neuroscience The analysis of kinematics, locomotion, and spatial tasks relies on the accurate detection of animal positions and pose. Pose and position can be assessed with video analysis programs, the “trackers.” Most available trackers represent animals as single points in space (no pose information available) or use markers to build a skeletal representation of pose. Markers are either physical objects attached to the body (white balls, stickers, or paint) or they are defined in silico using recognizable body structures (e.g., joints, limbs, color patterns). Physical markers often cannot be used if the animals are small, lack prominent body structures on which the markers can be placed, or live in environments such as aquatic ones that might detach the marker. Here, we introduce a marker-free pose-estimator (LACE Limbless Animal traCkEr) that builds the pose of the animal de novo from its contour. LACE detects the contour of the animal and derives the body mid-line, building a pseudo-skeleton by defining vertices and edges. By applying LACE to analyse the pose of larval Drosophila melanogaster and adult zebrafish, we illustrate that LACE allows to quantify, for example, genetic alterations of peristaltic movements and gender-specific locomotion patterns that are associated with different body shapes. As illustrated by these examples, LACE provides a versatile method for assessing position, pose and movement patterns, even in animals without limbs. Frontiers Media S.A. 2022-03-28 /pmc/articles/PMC8997243/ /pubmed/35418841 http://dx.doi.org/10.3389/fnbeh.2022.819146 Text en Copyright © 2022 Garg, André, Giraldo, Heyer, Göpfert, Dosch and Geurten. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Behavioral Neuroscience
Garg, Vranda
André, Selina
Giraldo, Diego
Heyer, Luisa
Göpfert, Martin C.
Dosch, Roland
Geurten, Bart R. H.
A Markerless Pose Estimator Applicable to Limbless Animals
title A Markerless Pose Estimator Applicable to Limbless Animals
title_full A Markerless Pose Estimator Applicable to Limbless Animals
title_fullStr A Markerless Pose Estimator Applicable to Limbless Animals
title_full_unstemmed A Markerless Pose Estimator Applicable to Limbless Animals
title_short A Markerless Pose Estimator Applicable to Limbless Animals
title_sort markerless pose estimator applicable to limbless animals
topic Behavioral Neuroscience
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8997243/
https://www.ncbi.nlm.nih.gov/pubmed/35418841
http://dx.doi.org/10.3389/fnbeh.2022.819146
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