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Pathfinder: open source software for analyzing spatial navigation search strategies

Spatial navigation is a universal behavior that varies depending on goals, experience and available sensory stimuli. Spatial navigational tasks are routinely used to study learning, memory and goal-directed behavior, in both animals and humans. One popular paradigm for testing spatial memory is the...

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Autores principales: Cooke, Matthew B., O'Leary, Timothy P., Harris, Phelan, Ma, Ricky, Brown, Richard E., Snyder, Jason S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6974928/
https://www.ncbi.nlm.nih.gov/pubmed/32025289
http://dx.doi.org/10.12688/f1000research.20352.2
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author Cooke, Matthew B.
O'Leary, Timothy P.
Harris, Phelan
Ma, Ricky
Brown, Richard E.
Snyder, Jason S.
author_facet Cooke, Matthew B.
O'Leary, Timothy P.
Harris, Phelan
Ma, Ricky
Brown, Richard E.
Snyder, Jason S.
author_sort Cooke, Matthew B.
collection PubMed
description Spatial navigation is a universal behavior that varies depending on goals, experience and available sensory stimuli. Spatial navigational tasks are routinely used to study learning, memory and goal-directed behavior, in both animals and humans. One popular paradigm for testing spatial memory is the Morris water maze, where subjects learn the location of a hidden platform that offers escape from a pool of water. Researchers typically express learning as a function of the latency to escape, though this reveals little about the underlying navigational strategies. Recently, a number of studies have begun to classify water maze search strategies in order to clarify the precise spatial and mnemonic functions of different brain regions, and to identify which aspects of spatial memory are disrupted in disease models. However, despite their usefulness, strategy analyses have not been widely adopted due to the lack of software to automate analyses. To address this need we developed Pathfinder, an open source application for analyzing spatial navigation behaviors. In a representative dataset, we show that Pathfinder effectively characterizes the development of highly-specific spatial search strategies as male and female mice learn a standard spatial water maze. Pathfinder can read data files from commercially- and freely-available software packages, is optimized for classifying search strategies in water maze paradigms, and can also be used to analyze 2D navigation by other species, and in other tasks, as long as timestamped xy coordinates are available. Pathfinder is simple to use, can automatically determine pool and platform geometry, generates heat maps, analyzes navigation with respect to multiple goal locations, and can be updated to accommodate future developments in spatial behavioral analyses. Given these features, Pathfinder may be a useful tool for studying how navigational strategies are regulated by the environment, depend on specific neural circuits, and are altered by pathology.
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spelling pubmed-69749282020-02-04 Pathfinder: open source software for analyzing spatial navigation search strategies Cooke, Matthew B. O'Leary, Timothy P. Harris, Phelan Ma, Ricky Brown, Richard E. Snyder, Jason S. F1000Res Software Tool Article Spatial navigation is a universal behavior that varies depending on goals, experience and available sensory stimuli. Spatial navigational tasks are routinely used to study learning, memory and goal-directed behavior, in both animals and humans. One popular paradigm for testing spatial memory is the Morris water maze, where subjects learn the location of a hidden platform that offers escape from a pool of water. Researchers typically express learning as a function of the latency to escape, though this reveals little about the underlying navigational strategies. Recently, a number of studies have begun to classify water maze search strategies in order to clarify the precise spatial and mnemonic functions of different brain regions, and to identify which aspects of spatial memory are disrupted in disease models. However, despite their usefulness, strategy analyses have not been widely adopted due to the lack of software to automate analyses. To address this need we developed Pathfinder, an open source application for analyzing spatial navigation behaviors. In a representative dataset, we show that Pathfinder effectively characterizes the development of highly-specific spatial search strategies as male and female mice learn a standard spatial water maze. Pathfinder can read data files from commercially- and freely-available software packages, is optimized for classifying search strategies in water maze paradigms, and can also be used to analyze 2D navigation by other species, and in other tasks, as long as timestamped xy coordinates are available. Pathfinder is simple to use, can automatically determine pool and platform geometry, generates heat maps, analyzes navigation with respect to multiple goal locations, and can be updated to accommodate future developments in spatial behavioral analyses. Given these features, Pathfinder may be a useful tool for studying how navigational strategies are regulated by the environment, depend on specific neural circuits, and are altered by pathology. F1000 Research Limited 2020-06-15 /pmc/articles/PMC6974928/ /pubmed/32025289 http://dx.doi.org/10.12688/f1000research.20352.2 Text en Copyright: © 2020 Cooke MB et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Cooke, Matthew B.
O'Leary, Timothy P.
Harris, Phelan
Ma, Ricky
Brown, Richard E.
Snyder, Jason S.
Pathfinder: open source software for analyzing spatial navigation search strategies
title Pathfinder: open source software for analyzing spatial navigation search strategies
title_full Pathfinder: open source software for analyzing spatial navigation search strategies
title_fullStr Pathfinder: open source software for analyzing spatial navigation search strategies
title_full_unstemmed Pathfinder: open source software for analyzing spatial navigation search strategies
title_short Pathfinder: open source software for analyzing spatial navigation search strategies
title_sort pathfinder: open source software for analyzing spatial navigation search strategies
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6974928/
https://www.ncbi.nlm.nih.gov/pubmed/32025289
http://dx.doi.org/10.12688/f1000research.20352.2
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