Computational protocol: SpotMetrics: An Open Source Image Analysis Software Plugin for Automatic Chromatophore Detection and Measurement

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Protocol publication

[…] SpotMetrics makes use of the following libraries which are used to detect, track, and measure the spot properties within a particular video:AVI_Reader ( is used to import and read video files (.avi format) of chromatophores or other objects of interest to be analyzed.TrackMate ( detects and tracks every spot for the entire length of the video. Also, TrackMate keeps a record of every spot's X, Y coordinates from every frame for later reference. Lastly, it allows users to filter out spots that are of no interest.Particle Analyzer ( analyzes and keeps track of the Regions of Interest (ROIs) in each frame and measures the area of each spot.Measure Color (author: George El Haddad) is a simple algorithm that retrieves the central X, Y coordinate of each spot (with the help of TrackMate) and return the Red, Green, and Blue (RGB) values for the spot.Apache POI ( is a fast and highly scalable library used to export data to a Microsoft Excel file (.xlsx). It is capable of generating large Excel files, depending on the amount of data to be exported. […]

Pipeline specifications

Software tools ImageJ, TrackMate
Application Microscopic phenotype analysis