DeepEthogram, a machine learning pipeline for supervised behavior classification from raw pixels
Videos of animal behavior are used to quantify researcher-defined behaviors of interest to study neural function, gene mutations, and pharmacological therapies. Behaviors of interest are often scored manually, which is time-consuming, limited to few behaviors, and variable across researchers. We cre...
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| Main Authors: | , , , , , , , , , , |
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| Language: | English |
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eLife Sciences Publications Ltd
02.09.2021
eLife Sciences Publications, Ltd |
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| ISSN: | 2050-084X, 2050-084X |
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| Abstract | Videos of animal behavior are used to quantify researcher-defined behaviors of interest to study neural function, gene mutations, and pharmacological therapies. Behaviors of interest are often scored manually, which is time-consuming, limited to few behaviors, and variable across researchers. We created DeepEthogram: software that uses supervised machine learning to convert raw video pixels into an ethogram, the behaviors of interest present in each video frame. DeepEthogram is designed to be general-purpose and applicable across species, behaviors, and video-recording hardware. It uses convolutional neural networks to compute motion, extract features from motion and images, and classify features into behaviors. Behaviors are classified with above 90% accuracy on single frames in videos of mice and flies, matching expert-level human performance. DeepEthogram accurately predicts rare behaviors, requires little training data, and generalizes across subjects. A graphical interface allows beginning-to-end analysis without end-user programming. DeepEthogram’s rapid, automatic, and reproducible labeling of researcher-defined behaviors of interest may accelerate and enhance supervised behavior analysis. Code is available at:
https://github.com/jbohnslav/deepethogram
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| AbstractList | Videos of animal behavior are used to quantify researcher-defined behaviors of interest to study neural function, gene mutations, and pharmacological therapies. Behaviors of interest are often scored manually, which is time-consuming, limited to few behaviors, and variable across researchers. We created DeepEthogram: software that uses supervised machine learning to convert raw video pixels into an ethogram, the behaviors of interest present in each video frame. DeepEthogram is designed to be general-purpose and applicable across species, behaviors, and video-recording hardware. It uses convolutional neural networks to compute motion, extract features from motion and images, and classify features into behaviors. Behaviors are classified with above 90% accuracy on single frames in videos of mice and flies, matching expert-level human performance. DeepEthogram accurately predicts rare behaviors, requires little training data, and generalizes across subjects. A graphical interface allows beginning-to-end analysis without end-user programming. DeepEthogram’s rapid, automatic, and reproducible labeling of researcher-defined behaviors of interest may accelerate and enhance supervised behavior analysis. Code is available at: https://github.com/jbohnslav/deepethogram. Videos of animal behavior are used to quantify researcher-defined behaviors of interest to study neural function, gene mutations, and pharmacological therapies. Behaviors of interest are often scored manually, which is time-consuming, limited to few behaviors, and variable across researchers. We created DeepEthogram: software that uses supervised machine learning to convert raw video pixels into an ethogram, the behaviors of interest present in each video frame. DeepEthogram is designed to be general-purpose and applicable across species, behaviors, and video-recording hardware. It uses convolutional neural networks to compute motion, extract features from motion and images, and classify features into behaviors. Behaviors are classified with above 90% accuracy on single frames in videos of mice and flies, matching expert-level human performance. DeepEthogram accurately predicts rare behaviors, requires little training data, and generalizes across subjects. A graphical interface allows beginning-to-end analysis without end-user programming. DeepEthogram's rapid, automatic, and reproducible labeling of researcher-defined behaviors of interest may accelerate and enhance supervised behavior analysis. Code is available at: https://github.com/jbohnslav/deepethogram.Videos of animal behavior are used to quantify researcher-defined behaviors of interest to study neural function, gene mutations, and pharmacological therapies. Behaviors of interest are often scored manually, which is time-consuming, limited to few behaviors, and variable across researchers. We created DeepEthogram: software that uses supervised machine learning to convert raw video pixels into an ethogram, the behaviors of interest present in each video frame. DeepEthogram is designed to be general-purpose and applicable across species, behaviors, and video-recording hardware. It uses convolutional neural networks to compute motion, extract features from motion and images, and classify features into behaviors. Behaviors are classified with above 90% accuracy on single frames in videos of mice and flies, matching expert-level human performance. DeepEthogram accurately predicts rare behaviors, requires little training data, and generalizes across subjects. A graphical interface allows beginning-to-end analysis without end-user programming. DeepEthogram's rapid, automatic, and reproducible labeling of researcher-defined behaviors of interest may accelerate and enhance supervised behavior analysis. Code is available at: https://github.com/jbohnslav/deepethogram. Videos of animal behavior are used to quantify researcher-defined behaviors of interest to study neural function, gene mutations, and pharmacological therapies. Behaviors of interest are often scored manually, which is time-consuming, limited to few behaviors, and variable across researchers. We created DeepEthogram: software that uses supervised machine learning to convert raw video pixels into an ethogram, the behaviors of interest present in each video frame. DeepEthogram is designed to be general-purpose and applicable across species, behaviors, and video-recording hardware. It uses convolutional neural networks to compute motion, extract features from motion and images, and classify features into behaviors. Behaviors are classified with above 90% accuracy on single frames in videos of mice and flies, matching expert-level human performance. DeepEthogram accurately predicts rare behaviors, requires little training data, and generalizes across subjects. A graphical interface allows beginning-to-end analysis without end-user programming. DeepEthogram’s rapid, automatic, and reproducible labeling of researcher-defined behaviors of interest may accelerate and enhance supervised behavior analysis. Code is available at: https://github.com/jbohnslav/deepethogram . |
| Author | Wimalasena, Nivanthika K Kashlan, Adam D Dai, Yu Y Yarmolinsky, David A Clausing, Kelsey J Orefice, Lauren L Chiappe, M Eugenia Bohnslav, James P Cruz, Tomás Woolf, Clifford J Harvey, Christopher D |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/34473051$$D View this record in MEDLINE/PubMed |
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| Keywords | deep learning mouse D. melanogaster neuroscience behavior analysis computer vision |
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