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A system for long-term high-resolution 3D tracking of movement kinematics in freely behaving animals

Award Number: R01GM136972
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 01/01/2021
PERIOD OF PERFORMANCE END DATE: 12/31/2025

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A system for long-term high-resolution 3D tracking of movement kinematics in freely behaving animals - PROJECT SUMMARY The aim of this proposal is to deliver an innovative and easy-to-use experimental platform for measuring and quantifying naturalistic behaviors of mammalian animal models used for biomedical research, including rodents and monkeys, across a range of spatial and temporal scales. This will require developing a method for tracking movements freely behaving animals with far higher spatiotemporal resolution and more kinematic detail than currently possible. To overcome the limitations of current technologies, a new solution is proposed that synergistically combines two methods - marker based motion capture and a video- based machine learning approach. First, using marker-based motion capture, the gold standard for 3D tracking in humans, the position of experimental subjects' head, trunk, and limbs will be tracked in 3D with submillimeter precision. An innovative marker design, placement strategy, and post-processing pipeline will ensure an unprecedentedly detailed description of rodent behavior over a large range of timescales. To make the system more efficient, robust, affordable and better suited for high-throughput longitudinal studies, the unprecedentedly rich and large 3D datasets generated by the motion capture experiments will be leveraged to train a deep neural network to predict pose and appendage positions from a set of 1-6 normal video cameras. To best capitalize on the large training datasets, the latest advances in convolutional neural networks for image analysis will be incorporated. Together, these advances will promote generalization of the high-resolution 3D tracking system to a variety of animals and environments, thus establishing a cheap, flexible, and easy-to use kinematic tracking method that can easily be scaled up and adopted by other labs. The large ground-truth datasets will allow the system to be benchmarked and compared against state-of-the art technologies in quantitative and rigorous ways. Preliminary studies have been very positive and suggest large improvements over current methods both when it comes to the range of behaviors that can be tracked and the precision with which they can be measured. Importantly, all new technology will be readily shared with the scientific community, thereby leveraging from this single grant the potential for numerous investigators to dramatically improve the efficiency of their research programs requiring rigorous quantitative descriptions of animal behavior.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2024 ( Subtotal = $397,654 )
2024	2024	PRESIDENT AND FELLOWS OF HARVARD COLLEGE	1033 MASSACHUSETTS AVE STE 3	CAMBRIDGE	MA	02138	MIDDLESEX	USA	Biomedical Research and Research Training	000	4	3/20/2024	NON-COMPETING CONTINUATION	$357,888
2024	2024	PRESIDENT AND FELLOWS OF HARVARD COLLEGE	1033 MASSACHUSETTS AVE STE 3	CAMBRIDGE	MA	02138	MIDDLESEX	USA	Biomedical Research and Research Training	001	4	6/17/2024	NON-COMPETING CONTINUATION	$39,766
														Subtotal = $397,654

Issue Date FY: 2023 ( Subtotal = $397,654 )
2023	2023	PRESIDENT AND FELLOWS OF HARVARD COLLEGE	1033 MASSACHUSETTS AVE 5TH FL	CAMBRIDGE	MA	02138	MIDDLESEX	USA	Biomedical Research and Research Training	000	3	12/19/2022	NON-COMPETING CONTINUATION	$357,889
2023	2023	PRESIDENT AND FELLOWS OF HARVARD COLLEGE	1033 MASSACHUSETTS AVE 5TH FL	CAMBRIDGE	MA	02138	MIDDLESEX	USA	Biomedical Research and Research Training	001	3	2/15/2023	NON-COMPETING CONTINUATION	$39,765
														Subtotal = $397,654

Issue Date FY: 2022 ( Subtotal = $651,154 )
2022	2022	PRESIDENT AND FELLOWS OF HARVARD COLLEGE	1033 MASSACHUSETTS AVE 5TH FL	CAMBRIDGE	MA	02138	MIDDLESEX	USA	Biomedical Research and Research Training	001	2	6/29/2022	NON-COMPETING CONTINUATION	$39,766
2022	2022	PRESIDENT AND FELLOWS OF HARVARD COLLEGE	1033 MASSACHUSETTS AVE 5TH FL	CAMBRIDGE	MA	02138	MIDDLESEX	USA	Biomedical Research and Research Training	000	2	12/23/2021	NON-COMPETING CONTINUATION	$357,888
2022	2022	PRESIDENT AND FELLOWS OF HARVARD COLLEGE	1033 MASSACHUSETTS AVE 5TH FL	CAMBRIDGE	MA	02138	MIDDLESEX	USA	Biomedical Research and Research Training	002	2	8/30/2022	SUPPLEMENT FOR EXPANSION	$253,500
														Subtotal = $651,154

Issue Date FY: 2021 ( Subtotal = $411,071 )
2021	2021	PRESIDENT AND FELLOWS OF HARVARD COLLEGE	1033 MASSACHUSETTS AVE 5TH FL	CAMBRIDGE	MA	02138	MIDDLESEX	USA	Biomedical Research and Research Training	000	1	12/10/2020	NEW	$411,071
														Subtotal = $411,071

Grand Total All Awards = $1,857,533

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A system for long-term high-resolution 3D tracking of movement kinematics in freely behaving animals

Award Number: R01GM136972

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 01/01/2021

PERIOD OF PERFORMANCE END DATE: 12/31/2025

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