Plant Image Analysis Plant Image Analysis

RTipC

Phenomics and Bioinformatics Research Centre @ University of South Australia
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Scientific article

Root phenotyping by root tip detection and classification through statistical learning
Kumar, P. Huang, C. Cai, J. Miklavcic, S.J.,
Plant and Soil, 380, Issue 1-2 , pp 193-209, March 2014.

View at publisher| Download PDF
Description

Root tip detection is an algorithm combining the use of structural information (root tip, segments, ...) and machine learning techniques to detect, count and classify the root tips of complex root systems.

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Overview
Operating system
windows, matlab,

Licence
freeware,

Measured variables
count, diameter,

Automation level
automated,

Plant requirements
any,

Image requirements
any,

Export formats
txt,

Other information
Requires Matlab executor to run

Additional information

Steps for running the executable for root tip detection

  1. Download and install Matlab compiler runtime for R2013q.

  2. Place the executable root_tip.exe and machine trained file zm_gmm4.mat and all the images in a folder together. Images should be in .tif file format. Five example files have been attached with this download.

  3. Now simply run the executable. It will read and process all the files in the folder and generate a result.txt file.

  4. The result.txt file has the counts of primary and lateral roots. It also has histogram of root tips as a function of root tip diameter. The last column is the count of root tips whose diameter could not be determined reliably.

  5. Please refer to the paper for details of implementation.