The Experts below are selected from a list of 99396 Experts worldwide ranked by ideXlab platform

Denise J Cai - One of the best experts on this subject based on the ideXlab platform.

  • eztrack an open source video analysis pipeline for the investigation of Animal Behavior
    Scientific Reports, 2019
    Co-Authors: Zachary T Pennington, Zhe Dong, Yu Feng, Lauren M Vetere, Lucia Pageharley, Tristan Shuman, Denise J Cai
    Abstract:

    Tracking Animal Behavior by video is one of the most common tasks in the life sciences. Although commercial software exists for executing this task, they often present enormous cost to the researcher and can entail purchasing hardware that is expensive and lacks adaptability. Additionally, the underlying code is often proprietary. Alternatively, available open-source options frequently require model training and can be challenging for those inexperienced with programming. Here we present an open-source and platform independent set of Behavior analysis pipelines using interactive Python that researchers with no prior programming experience can use. Two modules are described. One module can be used for the positional analysis of an individual Animal, amenable to a wide range of Behavioral tasks. A second module is described for the analysis of freezing Behavior. For both modules, a range of interactive plots and visualizations are available to confirm that chosen parameters produce the anticipated results. Moreover, batch processing tools for the fast analysis of multiple videos is provided, and frame-by-frame output makes alignment with biological recording data simple. Lastly, options for cropping video frames to mitigate the influence of fiberoptic/electrophysiology cables, analyzing specified portions of time, and defining regions of interest, are readily implemented.

  • eztrack an open source video analysis pipeline for the investigation of Animal Behavior
    bioRxiv, 2019
    Co-Authors: Zachary T Pennington, Zhe Dong, Yu Feng, Lauren M Vetere, Tristan Shuman, Regina Bowler, Denise J Cai
    Abstract:

    Abstract Tracking small Animal Behavior by video is one of the most common tasks in the fields of neuroscience and psychology. Although commercial software exists for the execution of this task, this software often presents enormous cost to the researcher, and can also entail purchasing specific hardware setups that are not only expensive but lack adaptability. Moreover, the inaccessibility of the code underlying this software renders them inflexible. Alternatively, available open source options frequently require extensive model training and can be challenging for those inexperienced with programming. Here we present an open source and platform independent set of Behavior analysis pipelines using interactive Python (iPython/Jupyter Notebook) that researchers with no prior programming experience can use. Two modules are described. One module can be used for the positional analysis of an individual Animal across a session (i.e., location tracking), amenable to a wide range of Behavioral tasks including conditioned place preference, water maze, light-dark box, open field, and elevated plus maze, to name but a few. A second module is described for the analysis of conditioned freezing Behavior. For both modules, a range of interactive plots and visualizations are available to confirm that chosen parameters produce results that conform to the user’s approval. In addition, batch processing tools for the fast analysis of multiple videos is provided, and frame-by-frame output makes aligning the data with neural recording data simple. Lastly, options for cropping video frames to mitigate the influence of fiberoptic/electrophysiology cables, analyzing specified portions of time in a video, and defining regions of interest, can be implemented with ease.

Clément Levallois - One of the best experts on this subject based on the ideXlab platform.

  • The Development of Sociobiology in relation to Animal Behavior Studies, 1946-1975
    Journal of the History of Biology, 2018
    Co-Authors: Clément Levallois
    Abstract:

    This paper aims at bridging a gap between the history of American Animal Behavior studies and the history of sociobiology. In the post-war period, ecology, comparative psychology and ethology were all investigating Animal societies, using different approaches ranging from fieldwork to laboratory studies. We argue that this disunity in “practices of place” (Kohler, Robert E. Landscapes & Labscapes: Exploring the Lab-Field Border in Biology. Chicago: University of Chicago Press, 2002) explains the attempts of dialogue between those three fields and early calls for unity through “sociobiology” by J. Paul Scott. In turn, tensions between the naturalist tradition and the rising reductionist approach in biology provide an original background for a history of Edward Wilson’s own version of sociobiology, much beyond the William Hamilton’s papers (Journal of Theoretical Biology 7: 1–16, 17–52, 1964) usually considered as its key antecedent. Naturalists were in a defensive position in the geography of the fields studying Animal Behavior, and in reaction were a driving force behind the various projects of synthesis called “sociobiology”.

  • The Development of Sociobiology in Relation to Animal Behavior Studies, 1946–1975
    Journal of the History of Biology, 2018
    Co-Authors: Clément Levallois
    Abstract:

    This paper aims at bridging a gap between the history of American Animal Behavior studies and the history of sociobiology. In the post-war period, ecology, comparative psychology and ethology were all investigating Animal societies, using different approaches ranging from fieldwork to laboratory studies. We argue that this disunity in “practices of place” (Kohler, Robert E. Landscapes & Labscapes: Exploring the Lab-Field Border in Biology . Chicago: University of Chicago Press, 2002 ) explains the attempts of dialogue between those three fields and early calls for unity through “sociobiology” by J. Paul Scott. In turn, tensions between the naturalist tradition and the rising reductionist approach in biology provide an original background for a history of Edward Wilson’s own version of sociobiology, much beyond the William Hamilton’s papers ( Journal of Theoretical Biology 7: 1–16, 17–52, 1964 ) usually considered as its key antecedent. Naturalists were in a defensive position in the geography of the fields studying Animal Behavior, and in reaction were a driving force behind the various projects of synthesis called “sociobiology”.

Zachary T Pennington - One of the best experts on this subject based on the ideXlab platform.

  • eztrack an open source video analysis pipeline for the investigation of Animal Behavior
    Scientific Reports, 2019
    Co-Authors: Zachary T Pennington, Zhe Dong, Yu Feng, Lauren M Vetere, Lucia Pageharley, Tristan Shuman, Denise J Cai
    Abstract:

    Tracking Animal Behavior by video is one of the most common tasks in the life sciences. Although commercial software exists for executing this task, they often present enormous cost to the researcher and can entail purchasing hardware that is expensive and lacks adaptability. Additionally, the underlying code is often proprietary. Alternatively, available open-source options frequently require model training and can be challenging for those inexperienced with programming. Here we present an open-source and platform independent set of Behavior analysis pipelines using interactive Python that researchers with no prior programming experience can use. Two modules are described. One module can be used for the positional analysis of an individual Animal, amenable to a wide range of Behavioral tasks. A second module is described for the analysis of freezing Behavior. For both modules, a range of interactive plots and visualizations are available to confirm that chosen parameters produce the anticipated results. Moreover, batch processing tools for the fast analysis of multiple videos is provided, and frame-by-frame output makes alignment with biological recording data simple. Lastly, options for cropping video frames to mitigate the influence of fiberoptic/electrophysiology cables, analyzing specified portions of time, and defining regions of interest, are readily implemented.

  • eztrack an open source video analysis pipeline for the investigation of Animal Behavior
    bioRxiv, 2019
    Co-Authors: Zachary T Pennington, Zhe Dong, Yu Feng, Lauren M Vetere, Tristan Shuman, Regina Bowler, Denise J Cai
    Abstract:

    Abstract Tracking small Animal Behavior by video is one of the most common tasks in the fields of neuroscience and psychology. Although commercial software exists for the execution of this task, this software often presents enormous cost to the researcher, and can also entail purchasing specific hardware setups that are not only expensive but lack adaptability. Moreover, the inaccessibility of the code underlying this software renders them inflexible. Alternatively, available open source options frequently require extensive model training and can be challenging for those inexperienced with programming. Here we present an open source and platform independent set of Behavior analysis pipelines using interactive Python (iPython/Jupyter Notebook) that researchers with no prior programming experience can use. Two modules are described. One module can be used for the positional analysis of an individual Animal across a session (i.e., location tracking), amenable to a wide range of Behavioral tasks including conditioned place preference, water maze, light-dark box, open field, and elevated plus maze, to name but a few. A second module is described for the analysis of conditioned freezing Behavior. For both modules, a range of interactive plots and visualizations are available to confirm that chosen parameters produce results that conform to the user’s approval. In addition, batch processing tools for the fast analysis of multiple videos is provided, and frame-by-frame output makes aligning the data with neural recording data simple. Lastly, options for cropping video frames to mitigate the influence of fiberoptic/electrophysiology cables, analyzing specified portions of time in a video, and defining regions of interest, can be implemented with ease.

Tristan Shuman - One of the best experts on this subject based on the ideXlab platform.

  • eztrack an open source video analysis pipeline for the investigation of Animal Behavior
    Scientific Reports, 2019
    Co-Authors: Zachary T Pennington, Zhe Dong, Yu Feng, Lauren M Vetere, Lucia Pageharley, Tristan Shuman, Denise J Cai
    Abstract:

    Tracking Animal Behavior by video is one of the most common tasks in the life sciences. Although commercial software exists for executing this task, they often present enormous cost to the researcher and can entail purchasing hardware that is expensive and lacks adaptability. Additionally, the underlying code is often proprietary. Alternatively, available open-source options frequently require model training and can be challenging for those inexperienced with programming. Here we present an open-source and platform independent set of Behavior analysis pipelines using interactive Python that researchers with no prior programming experience can use. Two modules are described. One module can be used for the positional analysis of an individual Animal, amenable to a wide range of Behavioral tasks. A second module is described for the analysis of freezing Behavior. For both modules, a range of interactive plots and visualizations are available to confirm that chosen parameters produce the anticipated results. Moreover, batch processing tools for the fast analysis of multiple videos is provided, and frame-by-frame output makes alignment with biological recording data simple. Lastly, options for cropping video frames to mitigate the influence of fiberoptic/electrophysiology cables, analyzing specified portions of time, and defining regions of interest, are readily implemented.

  • eztrack an open source video analysis pipeline for the investigation of Animal Behavior
    bioRxiv, 2019
    Co-Authors: Zachary T Pennington, Zhe Dong, Yu Feng, Lauren M Vetere, Tristan Shuman, Regina Bowler, Denise J Cai
    Abstract:

    Abstract Tracking small Animal Behavior by video is one of the most common tasks in the fields of neuroscience and psychology. Although commercial software exists for the execution of this task, this software often presents enormous cost to the researcher, and can also entail purchasing specific hardware setups that are not only expensive but lack adaptability. Moreover, the inaccessibility of the code underlying this software renders them inflexible. Alternatively, available open source options frequently require extensive model training and can be challenging for those inexperienced with programming. Here we present an open source and platform independent set of Behavior analysis pipelines using interactive Python (iPython/Jupyter Notebook) that researchers with no prior programming experience can use. Two modules are described. One module can be used for the positional analysis of an individual Animal across a session (i.e., location tracking), amenable to a wide range of Behavioral tasks including conditioned place preference, water maze, light-dark box, open field, and elevated plus maze, to name but a few. A second module is described for the analysis of conditioned freezing Behavior. For both modules, a range of interactive plots and visualizations are available to confirm that chosen parameters produce results that conform to the user’s approval. In addition, batch processing tools for the fast analysis of multiple videos is provided, and frame-by-frame output makes aligning the data with neural recording data simple. Lastly, options for cropping video frames to mitigate the influence of fiberoptic/electrophysiology cables, analyzing specified portions of time in a video, and defining regions of interest, can be implemented with ease.

Lauren M Vetere - One of the best experts on this subject based on the ideXlab platform.

  • eztrack an open source video analysis pipeline for the investigation of Animal Behavior
    Scientific Reports, 2019
    Co-Authors: Zachary T Pennington, Zhe Dong, Yu Feng, Lauren M Vetere, Lucia Pageharley, Tristan Shuman, Denise J Cai
    Abstract:

    Tracking Animal Behavior by video is one of the most common tasks in the life sciences. Although commercial software exists for executing this task, they often present enormous cost to the researcher and can entail purchasing hardware that is expensive and lacks adaptability. Additionally, the underlying code is often proprietary. Alternatively, available open-source options frequently require model training and can be challenging for those inexperienced with programming. Here we present an open-source and platform independent set of Behavior analysis pipelines using interactive Python that researchers with no prior programming experience can use. Two modules are described. One module can be used for the positional analysis of an individual Animal, amenable to a wide range of Behavioral tasks. A second module is described for the analysis of freezing Behavior. For both modules, a range of interactive plots and visualizations are available to confirm that chosen parameters produce the anticipated results. Moreover, batch processing tools for the fast analysis of multiple videos is provided, and frame-by-frame output makes alignment with biological recording data simple. Lastly, options for cropping video frames to mitigate the influence of fiberoptic/electrophysiology cables, analyzing specified portions of time, and defining regions of interest, are readily implemented.

  • eztrack an open source video analysis pipeline for the investigation of Animal Behavior
    bioRxiv, 2019
    Co-Authors: Zachary T Pennington, Zhe Dong, Yu Feng, Lauren M Vetere, Tristan Shuman, Regina Bowler, Denise J Cai
    Abstract:

    Abstract Tracking small Animal Behavior by video is one of the most common tasks in the fields of neuroscience and psychology. Although commercial software exists for the execution of this task, this software often presents enormous cost to the researcher, and can also entail purchasing specific hardware setups that are not only expensive but lack adaptability. Moreover, the inaccessibility of the code underlying this software renders them inflexible. Alternatively, available open source options frequently require extensive model training and can be challenging for those inexperienced with programming. Here we present an open source and platform independent set of Behavior analysis pipelines using interactive Python (iPython/Jupyter Notebook) that researchers with no prior programming experience can use. Two modules are described. One module can be used for the positional analysis of an individual Animal across a session (i.e., location tracking), amenable to a wide range of Behavioral tasks including conditioned place preference, water maze, light-dark box, open field, and elevated plus maze, to name but a few. A second module is described for the analysis of conditioned freezing Behavior. For both modules, a range of interactive plots and visualizations are available to confirm that chosen parameters produce results that conform to the user’s approval. In addition, batch processing tools for the fast analysis of multiple videos is provided, and frame-by-frame output makes aligning the data with neural recording data simple. Lastly, options for cropping video frames to mitigate the influence of fiberoptic/electrophysiology cables, analyzing specified portions of time in a video, and defining regions of interest, can be implemented with ease.