Leaf Extraction and Analysis Framework Graphical User Interface: Segmenting and Analyzing the Structure of Leaf Veins and Areoles    

Abstract

Interest in the structure and function of physical biological networks has spurred the development of a number of theoretical models that predict optimal network structures across a broad array of taxonomic groups, from mammals to plants. In many cases, direct tests of predicted network structure are impossible given the lack of suitable empirical methods to quantify physical network geometry with sufficient scope and resolution. There is a long history of empirical methods to quantify the network structure of plants, from roots, to xylem networks in shoots and within leaves. However, with few exceptions, current methods emphasize the analysis of portions of, rather than entire networks. Here, we introduce the Leaf Extraction and Analysis Framework Graphical User Interface (LEAF GUI), a user-assisted software tool that facilitates improved empirical understanding of leaf network structure. LEAF GUI takes images of leaves where veins have been enhanced relative to the background, and following a series of interactive thresholding and cleaning steps, returns a suite of statistics and information on the structure of leaf venation networks and areoles. Metrics include the dimensions, position, and connectivity of all network veins, and the dimensions, shape, and position of the areoles they surround. Available for free download, the LEAF GUI software promises to facilitate improved understanding of the adaptive and ecological significance of leaf vein network structure.

Corrigendum to: New handbook for standardised measurement of plant functional traits worldwide

“…Additional venation traits can be measured for more detailed investigations of leaf structure and function (see references below in the present Section). Dilcher (1974); Gardner (1975) ;; Price et al (2011).…”

A Journey Through a Leaf: Phenomics Analysis of Leaf Growth inArabidopsis thaliana

“…Quantification of leaf venation parameters are facilitated by dark-field images of cleared leaves, in which lignified mature xylem vessels stand out due to their light-scattering properties. These high-contrast pictures can be analyzed manually (Candela et al, 1999;González-Bayón et al, 2006;Rolland-Lagan et al, 2009) or with semi-automated analysis methods, such as LEAF GUI and LIMANI (Price et al, 2011;Dhondt et al, 2012). Different parameters can be extracted from these images, such as the total vascular length, vascular complexity (sum of the number of endpoints, branching points and vascular elements) and vascular density (vein length per unit leaf area) (Figure 3g).…”

phenoVein - A tool for leaf vein segmentation and analysis

“…In the software LeafGUI, vein width calculation is based on the determination of the vein area and depends on user-defined thresholds (Price et al, 2011(Price et al, , 2012. With the software tool NEFI (Dirnberger et al, 2015), the width of veins can be visualized by using a watershed algorithm, but no data or validation measurements of the algorithm were presented.…”

“…A general overview on plant image analysis tools is collected in an online database at http://www.plant-imageanalysis.org (Lobet et al, 2013). Programs allowing automated or semiautomated analysis of leaf venation parameters are, for example, a method to extract leaf venation patterns (Rolland-Lagan et al, 2009), the leaf extraction and analysis framework graphical user interface LeafGUI (Price et al, 2011), the leaf image analysis interface LIMANI (Dhondt et al, 2012), the user-interactive vessel generation analysis tool VESGEN (Vickerman et al, 2009;Parsons-Wingerter et al, 2014), and the software network extraction from images NEFI (Dirnberger et al, 2015). Nevertheless, for the analysis of large-scale leaf vein phenotyping experiments, there are certain needs that are only partly covered by each of the approaches and programs mentioned above.…”