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Three-dimensional neurophenotyping of adult zebrafish behavior.

Cachat J, Stewart A, Utterback E, Hart P, Gaikwad S, Wong K, Kyzar E, Wu N, Kalueff AV - PLoS ONE (2011)

Bottom Line: The present large-scale study applied the newest video-tracking and data-mining technologies to further examine zebrafish anxiety-like phenotypes.It also enables rapid optimization of video tracking settings to improve quantification of automated parameters, and suggests that spatiotemporal organization of zebrafish swimming activity can be affected by various experimental manipulations in a manner predicted by their anxiolytic or anxiogenic nature.Our approach markedly enhances the power of zebrafish behavioral analyses, providing innovative framework for high-throughput 3D phenotyping of adult zebrafish behavior.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacology and Neuroscience Program, Tulane Neurophenotyping Platform and Zebrafish Neuroscience Research Consortium, Tulane University Medical School, New Orleans, Louisiana, United States of America.

ABSTRACT
The use of adult zebrafish (Danio rerio) in neurobehavioral research is rapidly expanding. The present large-scale study applied the newest video-tracking and data-mining technologies to further examine zebrafish anxiety-like phenotypes. Here, we generated temporal and spatial three-dimensional (3D) reconstructions of zebrafish locomotion, globally assessed behavioral profiles evoked by several anxiogenic and anxiolytic manipulations, mapped individual endpoints to 3D reconstructions, and performed cluster analysis to reconfirm behavioral correlates of high- and low-anxiety states. The application of 3D swim path reconstructions consolidates behavioral data (while increasing data density) and provides a novel way to examine and represent zebrafish behavior. It also enables rapid optimization of video tracking settings to improve quantification of automated parameters, and suggests that spatiotemporal organization of zebrafish swimming activity can be affected by various experimental manipulations in a manner predicted by their anxiolytic or anxiogenic nature. Our approach markedly enhances the power of zebrafish behavioral analyses, providing innovative framework for high-throughput 3D phenotyping of adult zebrafish behavior.

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Three-dimensional (3D) temporal and spatial reconstructions of adult zebrafish swim paths rapidly expose overall affective phenotype.After indicated experimental manipulations (Fig. 3), zebrafish novel tank behavior was manually observed and video-tracked using EthoVision XT7 program. Raw track and behavioral endpoints were processed, formatted, and visualized in a 3D scatter plot using RapidMiner 5.0 software; traditional computer-generated two-dimensional (2D) swim path traces were placed at t = 0.0 s (top left part of each panel) for reference. Representative 3D reconstructions were selected by comparing swim paths of all subjects within a cohort, ranking them from 1 to n based on similarity to each other (low/no to high activity) and choosing the middle for the illustrations. For better visuality and consistency, fish used for spatial 3D imaging were the same as those used for the respective temporal 3D reconstructions. For a more detailed analysis of 3D reconstructions, the average velocity (m/s) of each fish was reflected by changes in color from blue to green, yellow and red, as the velocity increases. Note that any other computer-generated behavioral indices (Table S1 of Supporting Information) may be expressed in color on 3D reconstructions of zebrafish locomotion paths. Overall, these 3D traces reveal striking differences between zebrafish high- and low-anxiety behaviors, thereby enabling a rapid visualization and interpretation of the observed phenotypes.
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pone-0017597-g006: Three-dimensional (3D) temporal and spatial reconstructions of adult zebrafish swim paths rapidly expose overall affective phenotype.After indicated experimental manipulations (Fig. 3), zebrafish novel tank behavior was manually observed and video-tracked using EthoVision XT7 program. Raw track and behavioral endpoints were processed, formatted, and visualized in a 3D scatter plot using RapidMiner 5.0 software; traditional computer-generated two-dimensional (2D) swim path traces were placed at t = 0.0 s (top left part of each panel) for reference. Representative 3D reconstructions were selected by comparing swim paths of all subjects within a cohort, ranking them from 1 to n based on similarity to each other (low/no to high activity) and choosing the middle for the illustrations. For better visuality and consistency, fish used for spatial 3D imaging were the same as those used for the respective temporal 3D reconstructions. For a more detailed analysis of 3D reconstructions, the average velocity (m/s) of each fish was reflected by changes in color from blue to green, yellow and red, as the velocity increases. Note that any other computer-generated behavioral indices (Table S1 of Supporting Information) may be expressed in color on 3D reconstructions of zebrafish locomotion paths. Overall, these 3D traces reveal striking differences between zebrafish high- and low-anxiety behaviors, thereby enabling a rapid visualization and interpretation of the observed phenotypes.

Mentions: Several factors were critical for our research strategy (Fig. 1). First, we used the latest version of EthoVision XT7 software (Noldus IT, Wageningen, Netherlands) with manual event-based scoring during the video acquisition. This allowed us to precisely integrate manual and automated endpoints into a single track file, overcoming the methodological challenges of earlier zebrafish studies [56]. Secondly, by acquiring videos at the maximum sampling rate, we markedly increased the data density for each subject with raw track files containing spatiotemporal, movement and manual data points for every 0.033 s. Upon this realization, we attempted to reconstruct swim paths using this rich spatiotemporal information. We applied data-mining software (Rapid Miner 5.0, Rapid-I GmbH, Dortmund, Germany) that became available only recently, to visualize zebrafish swim paths. To comprehensively dissect adult zebrafish behavior, we compared the effects of multiple anxiogenic and anxiolytic experimental manipulations (Fig. 3), created three-dimensional (3D) reconstructions of swim paths (Fig. 2, 4–6) and performed hierarchical cluster analyses (Fig. 7). Taken together, these strategies enabled us to 1) improve data handling by consolidating raw data, 2) rapidly examine overall zebrafish behaviors, and 3) optimize video-tracking settings to more accurately detect the behaviors of interest. Furthermore, compared to traditional bar/line graphs or 2D traces, these 3D reconstructions provide intuitive representation of zebrafish activity which can be used for global evaluations and visualization of observed affective states (Fig. 6).


Three-dimensional neurophenotyping of adult zebrafish behavior.

Cachat J, Stewart A, Utterback E, Hart P, Gaikwad S, Wong K, Kyzar E, Wu N, Kalueff AV - PLoS ONE (2011)

Three-dimensional (3D) temporal and spatial reconstructions of adult zebrafish swim paths rapidly expose overall affective phenotype.After indicated experimental manipulations (Fig. 3), zebrafish novel tank behavior was manually observed and video-tracked using EthoVision XT7 program. Raw track and behavioral endpoints were processed, formatted, and visualized in a 3D scatter plot using RapidMiner 5.0 software; traditional computer-generated two-dimensional (2D) swim path traces were placed at t = 0.0 s (top left part of each panel) for reference. Representative 3D reconstructions were selected by comparing swim paths of all subjects within a cohort, ranking them from 1 to n based on similarity to each other (low/no to high activity) and choosing the middle for the illustrations. For better visuality and consistency, fish used for spatial 3D imaging were the same as those used for the respective temporal 3D reconstructions. For a more detailed analysis of 3D reconstructions, the average velocity (m/s) of each fish was reflected by changes in color from blue to green, yellow and red, as the velocity increases. Note that any other computer-generated behavioral indices (Table S1 of Supporting Information) may be expressed in color on 3D reconstructions of zebrafish locomotion paths. Overall, these 3D traces reveal striking differences between zebrafish high- and low-anxiety behaviors, thereby enabling a rapid visualization and interpretation of the observed phenotypes.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3049776&req=5

pone-0017597-g006: Three-dimensional (3D) temporal and spatial reconstructions of adult zebrafish swim paths rapidly expose overall affective phenotype.After indicated experimental manipulations (Fig. 3), zebrafish novel tank behavior was manually observed and video-tracked using EthoVision XT7 program. Raw track and behavioral endpoints were processed, formatted, and visualized in a 3D scatter plot using RapidMiner 5.0 software; traditional computer-generated two-dimensional (2D) swim path traces were placed at t = 0.0 s (top left part of each panel) for reference. Representative 3D reconstructions were selected by comparing swim paths of all subjects within a cohort, ranking them from 1 to n based on similarity to each other (low/no to high activity) and choosing the middle for the illustrations. For better visuality and consistency, fish used for spatial 3D imaging were the same as those used for the respective temporal 3D reconstructions. For a more detailed analysis of 3D reconstructions, the average velocity (m/s) of each fish was reflected by changes in color from blue to green, yellow and red, as the velocity increases. Note that any other computer-generated behavioral indices (Table S1 of Supporting Information) may be expressed in color on 3D reconstructions of zebrafish locomotion paths. Overall, these 3D traces reveal striking differences between zebrafish high- and low-anxiety behaviors, thereby enabling a rapid visualization and interpretation of the observed phenotypes.
Mentions: Several factors were critical for our research strategy (Fig. 1). First, we used the latest version of EthoVision XT7 software (Noldus IT, Wageningen, Netherlands) with manual event-based scoring during the video acquisition. This allowed us to precisely integrate manual and automated endpoints into a single track file, overcoming the methodological challenges of earlier zebrafish studies [56]. Secondly, by acquiring videos at the maximum sampling rate, we markedly increased the data density for each subject with raw track files containing spatiotemporal, movement and manual data points for every 0.033 s. Upon this realization, we attempted to reconstruct swim paths using this rich spatiotemporal information. We applied data-mining software (Rapid Miner 5.0, Rapid-I GmbH, Dortmund, Germany) that became available only recently, to visualize zebrafish swim paths. To comprehensively dissect adult zebrafish behavior, we compared the effects of multiple anxiogenic and anxiolytic experimental manipulations (Fig. 3), created three-dimensional (3D) reconstructions of swim paths (Fig. 2, 4–6) and performed hierarchical cluster analyses (Fig. 7). Taken together, these strategies enabled us to 1) improve data handling by consolidating raw data, 2) rapidly examine overall zebrafish behaviors, and 3) optimize video-tracking settings to more accurately detect the behaviors of interest. Furthermore, compared to traditional bar/line graphs or 2D traces, these 3D reconstructions provide intuitive representation of zebrafish activity which can be used for global evaluations and visualization of observed affective states (Fig. 6).

Bottom Line: The present large-scale study applied the newest video-tracking and data-mining technologies to further examine zebrafish anxiety-like phenotypes.It also enables rapid optimization of video tracking settings to improve quantification of automated parameters, and suggests that spatiotemporal organization of zebrafish swimming activity can be affected by various experimental manipulations in a manner predicted by their anxiolytic or anxiogenic nature.Our approach markedly enhances the power of zebrafish behavioral analyses, providing innovative framework for high-throughput 3D phenotyping of adult zebrafish behavior.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacology and Neuroscience Program, Tulane Neurophenotyping Platform and Zebrafish Neuroscience Research Consortium, Tulane University Medical School, New Orleans, Louisiana, United States of America.

ABSTRACT
The use of adult zebrafish (Danio rerio) in neurobehavioral research is rapidly expanding. The present large-scale study applied the newest video-tracking and data-mining technologies to further examine zebrafish anxiety-like phenotypes. Here, we generated temporal and spatial three-dimensional (3D) reconstructions of zebrafish locomotion, globally assessed behavioral profiles evoked by several anxiogenic and anxiolytic manipulations, mapped individual endpoints to 3D reconstructions, and performed cluster analysis to reconfirm behavioral correlates of high- and low-anxiety states. The application of 3D swim path reconstructions consolidates behavioral data (while increasing data density) and provides a novel way to examine and represent zebrafish behavior. It also enables rapid optimization of video tracking settings to improve quantification of automated parameters, and suggests that spatiotemporal organization of zebrafish swimming activity can be affected by various experimental manipulations in a manner predicted by their anxiolytic or anxiogenic nature. Our approach markedly enhances the power of zebrafish behavioral analyses, providing innovative framework for high-throughput 3D phenotyping of adult zebrafish behavior.

Show MeSH