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CarrotSweeper

Digital image-based phenotyping platform to analyze carrot root shape attributes.

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Background

Summary

CarrotSweeper Pipeline

There are two main sub-directories to perform the major image analysis tasks:

The carrot-straightener directory contains the functions required to generate a midline from the image masks, and then run a straightening algorithm of that mask.

The pca-tools directory contains the analysis functions to measure and quantify the straightened masks.

Getting Started

Dependencies

  • MATLAB R2020A (recommended, but likely works on most older versions)
  • Image Processing Toolbox
  • Statistics and Learning Toolbox

This repository uses many functions from my other GitHub repo, HypoQuantyl (HQ). The full list of functions taken from HQ are found in the dependencies text file in the main directory of this repo.

Installation

Clone this repository to your file system, then simply add carrotsweeper to your MATLAB search path.

git clone https://github.com/jbustamante35/carrotsweeper

Author

Julian Bustamante, Cellular and Molecular Biology (jbustamante@wisc.edu)
University of Wisconsin - Madison
Department of Botany