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BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking

Quantitative descriptions of animal behavior are essential to study the neural substrates of cognitive and emotional processes. Analyses of naturalistic behaviors are often performed by hand or with expensive, inflexible commercial software. Recently, machine learning methods for markerless pose est...

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Autores principales: Gabriel, Christopher J, Zeidler, Zachary, Jin, Benita, Guo, Changliang, Goodpaster, Caitlin M, Kashay, Adrienne Q, Wu, Anna, Delaney, Molly, Cheung, Jovian, DiFazio, Lauren E, Sharpe, Melissa J, Aharoni, Daniel, Wilke, Scott A, DeNardo, Laura A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9398447/
https://www.ncbi.nlm.nih.gov/pubmed/35997072
http://dx.doi.org/10.7554/eLife.74314
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author Gabriel, Christopher J
Zeidler, Zachary
Jin, Benita
Guo, Changliang
Goodpaster, Caitlin M
Kashay, Adrienne Q
Wu, Anna
Delaney, Molly
Cheung, Jovian
DiFazio, Lauren E
Sharpe, Melissa J
Aharoni, Daniel
Wilke, Scott A
DeNardo, Laura A
author_facet Gabriel, Christopher J
Zeidler, Zachary
Jin, Benita
Guo, Changliang
Goodpaster, Caitlin M
Kashay, Adrienne Q
Wu, Anna
Delaney, Molly
Cheung, Jovian
DiFazio, Lauren E
Sharpe, Melissa J
Aharoni, Daniel
Wilke, Scott A
DeNardo, Laura A
author_sort Gabriel, Christopher J
collection PubMed
description Quantitative descriptions of animal behavior are essential to study the neural substrates of cognitive and emotional processes. Analyses of naturalistic behaviors are often performed by hand or with expensive, inflexible commercial software. Recently, machine learning methods for markerless pose estimation enabled automated tracking of freely moving animals, including in labs with limited coding expertise. However, classifying specific behaviors based on pose data requires additional computational analyses and remains a significant challenge for many groups. We developed BehaviorDEPOT (DEcoding behavior based on POsitional Tracking), a simple, flexible software program that can detect behavior from video timeseries and can analyze the results of experimental assays. BehaviorDEPOT calculates kinematic and postural statistics from keypoint tracking data and creates heuristics that reliably detect behaviors. It requires no programming experience and is applicable to a wide range of behaviors and experimental designs. We provide several hard-coded heuristics. Our freezing detection heuristic achieves above 90% accuracy in videos of mice and rats, including those wearing tethered head-mounts. BehaviorDEPOT also helps researchers develop their own heuristics and incorporate them into the software’s graphical interface. Behavioral data is stored framewise for easy alignment with neural data. We demonstrate the immediate utility and flexibility of BehaviorDEPOT using popular assays including fear conditioning, decision-making in a T-maze, open field, elevated plus maze, and novel object exploration.
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spelling pubmed-93984472022-08-24 BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking Gabriel, Christopher J Zeidler, Zachary Jin, Benita Guo, Changliang Goodpaster, Caitlin M Kashay, Adrienne Q Wu, Anna Delaney, Molly Cheung, Jovian DiFazio, Lauren E Sharpe, Melissa J Aharoni, Daniel Wilke, Scott A DeNardo, Laura A eLife Neuroscience Quantitative descriptions of animal behavior are essential to study the neural substrates of cognitive and emotional processes. Analyses of naturalistic behaviors are often performed by hand or with expensive, inflexible commercial software. Recently, machine learning methods for markerless pose estimation enabled automated tracking of freely moving animals, including in labs with limited coding expertise. However, classifying specific behaviors based on pose data requires additional computational analyses and remains a significant challenge for many groups. We developed BehaviorDEPOT (DEcoding behavior based on POsitional Tracking), a simple, flexible software program that can detect behavior from video timeseries and can analyze the results of experimental assays. BehaviorDEPOT calculates kinematic and postural statistics from keypoint tracking data and creates heuristics that reliably detect behaviors. It requires no programming experience and is applicable to a wide range of behaviors and experimental designs. We provide several hard-coded heuristics. Our freezing detection heuristic achieves above 90% accuracy in videos of mice and rats, including those wearing tethered head-mounts. BehaviorDEPOT also helps researchers develop their own heuristics and incorporate them into the software’s graphical interface. Behavioral data is stored framewise for easy alignment with neural data. We demonstrate the immediate utility and flexibility of BehaviorDEPOT using popular assays including fear conditioning, decision-making in a T-maze, open field, elevated plus maze, and novel object exploration. eLife Sciences Publications, Ltd 2022-08-23 /pmc/articles/PMC9398447/ /pubmed/35997072 http://dx.doi.org/10.7554/eLife.74314 Text en © 2022, Gabriel et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Neuroscience
Gabriel, Christopher J
Zeidler, Zachary
Jin, Benita
Guo, Changliang
Goodpaster, Caitlin M
Kashay, Adrienne Q
Wu, Anna
Delaney, Molly
Cheung, Jovian
DiFazio, Lauren E
Sharpe, Melissa J
Aharoni, Daniel
Wilke, Scott A
DeNardo, Laura A
BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking
title BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking
title_full BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking
title_fullStr BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking
title_full_unstemmed BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking
title_short BehaviorDEPOT is a simple, flexible tool for automated behavioral detection based on markerless pose tracking
title_sort behaviordepot is a simple, flexible tool for automated behavioral detection based on markerless pose tracking
topic Neuroscience
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9398447/
https://www.ncbi.nlm.nih.gov/pubmed/35997072
http://dx.doi.org/10.7554/eLife.74314
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