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    Cross Sectional Analyzer

    Authors: Thalia Barr-Malec, Nalin Richardson, and Matthew Rothman

    Date: 2020/05/14


    You can access the source files at 1.


    1. Unzip ‘Cross-sectional-analysis.zip,’ and locate Cross_Sectional_Analyzer.jar.

    2. Open the package contents of ImageJ, and navigate to ImageJ/plugins/Filters.

    3. Put Cross_Sectional_Analyzer.jar inside the ImageJ/plugins/Filters folder, and restart imageJ.

    4. Once ImageJ opens, open an image to analyze, and calibrate the image. To run the plugin, use Plugins>Filters>Cross Sectional Analyzer.

    Description: This plugin takes in an image of muscle fibers, outlines and numbers all of the fibers, and outputs a table of each fiber’s area as well as an RGB Color image of the numbered fiber outlines on a black background.

    Input Image Output Image