Track-a-worm, an open-source system for quantitative assessment of C. elegans locomotory and bending behavior

A major challenge of neuroscience is to understand the circuit and gene bases of behavior. C. elegans is commonly used as a model system to investigate how various gene products function at specific tissue, cellular, and synaptic foci to produce complicated locomotory and bending behavior. The inves...

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Veröffentlicht in:PloS one 2013-07, Vol.8 (7), p.e69653-e69653
Hauptverfasser: Wang, Sijie Jason, Wang, Zhao-Wen
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description A major challenge of neuroscience is to understand the circuit and gene bases of behavior. C. elegans is commonly used as a model system to investigate how various gene products function at specific tissue, cellular, and synaptic foci to produce complicated locomotory and bending behavior. The investigation generally requires quantitative behavioral analyses using an automated single-worm tracker, which constantly records and analyzes the position and body shape of a freely moving worm at a high magnification. Many single-worm trackers have been developed to meet lab-specific needs, but none has been widely implemented for various reasons, such as hardware difficult to assemble, and software lacking sufficient functionality, having closed source code, or using a programming language that is not broadly accessible. The lack of a versatile system convenient for wide implementation makes data comparisons difficult and compels other labs to develop new worm trackers. Here we describe Track-A-Worm, a system rich in functionality, open in source code, and easy to use. The system includes plug-and-play hardware (a stereomicroscope, a digital camera and a motorized stage), custom software written to run with Matlab in Windows 7, and a detailed user manual. Grayscale images are automatically converted to binary images followed by head identification and placement of 13 markers along a deduced spline. The software can extract and quantify a variety of parameters, including distance traveled, average speed, distance/time/speed of forward and backward locomotion, frequency and amplitude of dominant bends, overall bending activities measured as root mean square, and sum of all bends. It also plots worm travel path, bend trace, and bend frequency spectrum. All functionality is performed through graphical user interfaces and data is exported to clearly-annotated and documented Excel files. These features make Track-A-Worm a good candidate for implementation in other labs.
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C. elegans is commonly used as a model system to investigate how various gene products function at specific tissue, cellular, and synaptic foci to produce complicated locomotory and bending behavior. The investigation generally requires quantitative behavioral analyses using an automated single-worm tracker, which constantly records and analyzes the position and body shape of a freely moving worm at a high magnification. Many single-worm trackers have been developed to meet lab-specific needs, but none has been widely implemented for various reasons, such as hardware difficult to assemble, and software lacking sufficient functionality, having closed source code, or using a programming language that is not broadly accessible. The lack of a versatile system convenient for wide implementation makes data comparisons difficult and compels other labs to develop new worm trackers. Here we describe Track-A-Worm, a system rich in functionality, open in source code, and easy to use. The system includes plug-and-play hardware (a stereomicroscope, a digital camera and a motorized stage), custom software written to run with Matlab in Windows 7, and a detailed user manual. Grayscale images are automatically converted to binary images followed by head identification and placement of 13 markers along a deduced spline. The software can extract and quantify a variety of parameters, including distance traveled, average speed, distance/time/speed of forward and backward locomotion, frequency and amplitude of dominant bends, overall bending activities measured as root mean square, and sum of all bends. It also plots worm travel path, bend trace, and bend frequency spectrum. All functionality is performed through graphical user interfaces and data is exported to clearly-annotated and documented Excel files. 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subjects Animals
Automation
Behavior, Animal - physiology
Bends
Biology
Caenorhabditis elegans
Caenorhabditis elegans - physiology
Calibration
Computer programs
Computer Science
Digital cameras
Engineering
Frequency spectrum
Graphical user interface
Hardware
Imaging, Three-Dimensional
Interfaces
Localization
Locomotion
Locomotion - physiology
Nematodes
Nervous system
Neurons
Operating systems
Programming languages
Software
Source code
User interfaces
Worms
title Track-a-worm, an open-source system for quantitative assessment of C. elegans locomotory and bending behavior
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