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Resources » Paper

Graves J et al. (2010) Neuronal Development, Synaptic Function and Behavior, Madison, WI "Fast and Customizable Video Analysis of C. Elegans Locomotion"

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  • Comments on Graves J et al. (2010) Neuronal Development, Synaptic Function and Behavior, Madison, WI "Fast and Customizable Video Analysis of C. Elegans Locomotion" (0)

  • Overview

    Status:
    Publication type:
    Meeting_abstract
    WormBase ID:
    WBPaper00037350

    Graves J, & Mailler R (2010). Fast and Customizable Video Analysis of C. Elegans Locomotion presented in Neuronal Development, Synaptic Function and Behavior, Madison, WI. Unpublished information; cite only with author permission.

    Currently, various software solutions exist to analyze and extract features from videos of the worm C. Elegans. However, these software packages have not been widely accepted by the community because they implement a single process for converting video into data, are implemented using Matlab's outdated, undocumented image processing algorithms, tend to be slow, and are poorly documented. The software we have developed rectifies these deficiencies by providing a versatile toolkit of video analysis techniques where the end user can customize the analysis pipeline. Our software, written in Java, not only provides versions of the image analysis algorithms found in current software packages, it also provides alternate and improved techniques to allow the user to mix and match processing steps to accommodate their specific needs. These algorithms include gray-scale conversion, histogram analysis, noise reduction, contrast adjustment, binarization, thinning, edge detection, straight line and spline fitting, as well as polygonalization. To facilitate the pipeline creation and management process, our program provides an intuitive drag and drop interface that allows a user to select processing algorithms, set their parameters, and connect them together. Users can then test and refine their pipeline by viewing the video at each stage of processing. The output of the process is a standardized file format that contains the key characteristics of the worm's motion in a format that is compatible with statistical analysis software.


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