Tomato Analyzer: A Useful Software Application to Collect Accurate and Detailed Morphological and Colorimetric Data from Two-dimensional Objects

Abstract

Measuring fruit morphology and color traits of vegetable and fruit crops in an objective and reproducible way is important for detailed phenotypic analyses of these traits. Tomato Analyzer (TA) is a software program that measures 37 attributes related to two-dimensional shape in a semi-automatic and reproducible manner 1,2 . Many of these attributes, such as angles at the distal and proximal ends of the fruit and areas of indentation, are difficult to quantify manually. The attributes are organized in ten categories within the software: Basic Measurement, Fruit Shape Index, Blockiness, Homogeneity, Proximal Fruit End Shape, Distal Fruit End Shape, Asymmetry, Internal Eccentricity, Latitudinal Section and Morphometrics. The last category requires neither prior knowledge nor predetermined notions of the shape attributes, so morphometric analysis offers an unbiased option that may be better adapted to high-throughput analyses than attribute analysis. TA also offers the Color Test application that was designed to collect color measurements from scanned images and allow scanning devices to be calibrated using color standards 3 .TA provides several options to export and analyze shape attribute, morphometric, and color data. The data may be exported to an excel file in batch mode (more than 100 images at one time) or exported as individual images. The user can choose between output that displays the average for each attribute for the objects in each image (including standard deviation), or an output that displays the attribute values for each object on the image. TA has been a valuable and effective tool for indentifying and confirming tomato fruit shape Quantitative Trait Loci (QTL), as well as performing in-depth analyses of the effect of key fruit shape genes on plant morphology. Also, TA can be used to objectively classify fruit into various shape categories. Lastly, fruit shape and color traits in other plant species as well as other plant organs such as leaves and seeds can be evaluated with TA. Video LinkThe video component of this article can be found at http://www.jove.com/video/1856/ ProtocolTomato Analyzer (TA) software is designed to recognize objects of a certain size and image resolution, measured in dots (pixels) per inch (dpi). The software automatically determines the boundaries of fruit in a scanned image. The object boundary is determined through contour tracing, which results in a list of adjacent points describing the border of an object in an image. All fruit shape measurements are calculated based on the boundaries. The color test module "Tomato Analyzer Color Test" is designed to quantify the color parameters inside the boundaries recognized by the software. The color measurements are based on the RGB color space: R (red), G (green), and B (Blue). The average RGB values for each pixel is taken by Color test module and then translated to the CIELAB color space which uses L*, a*, b* to describe color in a way that approximates human visual perception. The Color test module calculates Hu...

Characterization of a collection of local varieties of tomato (Solanum lycopersicum L.) using conventional descriptors and the high-throughput phenomics tool Tomato Analyzer

“…The phenomics study performed with the high-throughput Tomato Analyzer software tool allowed the automatic acquisition of data for many fruit morphology traits not dealt with by the conventional descriptors (Brewer et al 2006, Gonzalo and van der Knaap 2008, Rodríguez et al 2010a, 2010b, Strecker et al 2010. This made possible the precise description of fruit morphology and detecting many differences for fruit morphology among accessions.…”

“…Recently, a free high-throughput phenomics software tool (Tomato Analyzer) for the analysis of fruit shape and flesh colour of tomato has been developed (Brewer et al 2006, Gonzalo and van der Knaap 2008, Rodríguez et al 2010a, 2010b, Strecker et al 2010. Tomato Analyzer allows scoring a large number of fruit shape and flesh colour traits from scanned images of fruit sections.…”

The control of tomato fruit elongation orchestrated by sun, ovate and fs8.1 in a wild relative of tomato

“…Anthesis flowers were hand pollinated and tagged in the field. Developing fruit were collected 10 days post anthesis (dpa) and at the ripening stage, cut longitudinally, scanned at 300 dpi, and analyzed for fruit shape using Tomato Analyzer v3.0 [11]. The specific attributes that were measured were shape index, distal end angle, obovoid and proximal eccentricity.…”

Analysis of variability and phylogeny in pisum (Pisum spp.) using digital phenotyping and morphological traits

“…Colour traits where measured on twodimensional digital images of 600 dpi taken on a Samsung CLX 3300 scanner of samples of 50 seeds or 20 pods per repetition and analysed using Tomato Analyzer (TA) software (Rodríguez et al, 2010). The colour traits were the two colour coordinates (a and b), as well as a psychometric index of lightness (L) from the CieLab system of colour; the parameters RGB (red, green and blue), the Hue angle value and the Chroma index, where: a coordinate indicates the greenness-redness of the colour (-a is green, +a is red) and varies between -128 and 128; b coordinate indicates blueness-yellowness of the colour (-b is blue, +b is yellow) and varies between -128 and 128; L is an approximate measurement of luminosity, which is the property according to which each colour can be considered as equivalent to a member of the greyscale, between black and white; Chroma is the difference of a hue in comparison to a grey colour with the same lightness (the higher the Chroma values, the higher is the colour intensity of samples perceived by humans) and Hue angle defines the pure colour and mixtures of them in a continuum that range from 0º to 359º.…”