Digital Phenotyping for Tomato Fruit Size, Shape, and Color


David M. Francis, The Ohio State University; Heather L. Merk, The Ohio State University

The TomatoAnalyzer software is designed to collect objective data from digital images. The software is capable of recognizing cross or longitudinal sections of fruit. Measuring morphological characteristics through image analysis increases the objectivity of phenotypic evaluations and provides data that are compatible with ontologies and databases intended to link phenotype to genotype.


The TomatoAnalyzer software was developed in conjunction with a controlled vocabulary to describe the shape and size of tomato fruit (Brewer et al., 2006). The software has been expanded to translate color data from the RGB system into the L*a*b* universal color space (Darrigues et al., 2008). Shape, size, and color descriptions are now incorporated into the trait and phenotype ontologies implemented in the Sol Genomics Network (SGN).

Although originally designed for use with tomato fruit, the software is flexible and can be used for other fruit and vegetables.


A tutorial describing image preparation and use of the TomatoAnalyzer software is available through the Journal of Visualized Experiments (JoVE) (Rodriguez et al., 2010). This video and the accompanying manuscript provide step-by-step instructions.

Figure 1. TomatoAnalyzer tutorial on JoVE. Screenshot Credit: Heather Merk, The Ohio State University.


Manuals and software for version 3.0 and version 2.2 are available for download. The software is designed to work with Windows 2000 or higher.

References Cited

  • Brewer, M. T., L. Lang, K. Fujimura, N. Dujmovic, S. Gray, and E. van der Knaap. 2006. Development of a controlled vocabulary and software application to analyze fruit shape variation in tomato and other plant species. Plant Physiology 141: 15–25. (Available online at: (verified 5 Jan 2011).
  • Darrigues, A., J. Hall, E. van der Knaap, and D. M. Francis. 2008. Tomato Analyzer-Color Test: a new tool for efficient digital phenotyping. Journal of the American Society for Horticultural Science 133: 579–586. (Available online at: (verified 31 Dec 2010).
  • Gonzalo, M. J., M. T. Brewer, C. Anderson, D. Sullivan, S. Gray, and E. J. van der Knaap. 2009. Tomato fruit shape analysis using morphometric and morphology attributes implemented in Tomato Analyzer software program. Journal of the American Society for Horticultural Science 134: 77–87. (Available online at: (verified 31 Dec 2010).
  • Rodríguez, G. R., J. B. Moyseenko, M. D. Robbins, N. Huarachi Morejón, D. M. Francis, and E. van der Knaap. 2010. Tomato Analyzer: A useful software application to collect accurate and detailed morphological and colorimetric data from two-dimensional objects. Journal of Visualized Experiments 37. (Available online at: (verified 5 Jan 2011).

External Links

Funding Statement

Development of this page was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.

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