Digital image-based phenotyping platform to analyze carrot root shape
attributes.
Refer to the publication resulting from this study:
A Digital Image-Based Phenotyping Platform for Analyzing Root Shape
Attributes in Carrot
[Figure 1 from referenced paper] Workflow outlining the pre-processing of carrot root images. (A) Each black-bordered box within the overall image are identified; (B) QR codes within the upper portion of each box are scanned and the encoded text is displayed as a form of quality control; (C) carrot pixels are distinguished from background pixels to generate binary masks; (D) the midline of the carrot root is estimated by tracing a path from the carrot tip to the center of the shoulder, following the maximum of the smoothed Euclidean distance transform; (E) width measurements are made by sampling the binary mask normal to vectors tangent to the midline; (F,G) A random forest classifier is used to detect the point at which to “de-tip” any residual, unexpanded tap root.*
The image pre-processing pipeline to obtain binary masks of carrot images can be found in the carrot-phenotyping repository
- MATLAB Version
- This tool was developed on Matlab R2020a. Versions slightly earlier or later should work fine but are not guaranteed.
- MATLAB Toolboxes
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.
Clone this repository to your file system, then simply add carrotsweeper to your MATLAB search path with sub-folders.
git clone https://github.com/jbustamante35/carrotsweeperThere 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 on that mask. Straightening begins from the tip of the carrot, which we identify uring a custom tip-finding algorithm.
The pca-tools directory contains the analysis functions to measure and quantify phenotypes such as curvature, width profiles, PCA, etc.
Julian Bustamante, PhD Researcher in Cellular and Molecular Biology
(jbustamante@wisc.edu)
University of Wisconsin - Madison, Department of Botany
Scott Brainard, PhD Researcher in Plant Breeding and Genetics
University of Wisconsin - Madison, Department of Horticulture