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Cross Sectional Analyzer

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


  1. Download, unzip it 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 PluginsFiltersCross Sectional Analyzer.