Plant Identification Based on Leaf Midrib Cross-Section Images Using Fractal Descriptors
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RESEARCH ARTICLE Plant Identification Based on Leaf Midrib Cross-Section Images Using Fractal Descriptors Núbia Rosa da Silva1,2,João Batista Florindo1, María Cecilia Gómez1,3, Davi Rodrigo Rossatto4, Rosana Marta Kolb5, Odemir Martinez Bruno1,2* 1 São Carlos Institute of Physics, University of São Paulo, PO Box 369, 13560-970, São Carlos, SP, Brazil, 2 Institute of Mathematics and Computer Science, University of São Paulo, USP, São Carlos, São Paulo, Brazil, 3 Department of Physics, Faculty of Biochemistry and Biological Sciences, National University of a11111 Littoral, Santa Fe, Argentina, 4 Department of Applied Biology, Faculty of Agriculture and Veterinary Sciences, Univ Estadual Paulista, UNESP, Jaboticabal, São Paulo, Brazil, 5 Department of Biological Sciences, Faculty of Sciences and Letters, Univ Estadual Paulista, UNESP, Assis, São Paulo, Brazil * [email protected] OPEN ACCESS Abstract Citation: da Silva NR, Florindo JB, Gómez MC, The correct identification of plants is a common necessity not only to researchers but also to Rossatto DR, Kolb RM, Bruno OM (2015) Plant Identification Based on Leaf Midrib Cross-Section the lay public. Recently, computational methods have been employed to facilitate this task, Images Using Fractal Descriptors. PLoS ONE 10(6): however, there are few studies front of the wide diversity of plants occurring in the world. e0130014. doi:10.1371/journal.pone.0130014 This study proposes to analyse images obtained from cross-sections of leaf midrib using Academic Editor: Helmut Ahammer, Medical fractal descriptors. These descriptors are obtained from the fractal dimension of the object University of Graz, AUSTRIA computed at a range of scales. In this way, they provide rich information regarding the spa- Received: January 19, 2015 tial distribution of the analysed structure and, as a consequence, they measure the multi- Accepted: May 15, 2015 scale morphology of the object of interest. In Biology, such morphology is of great importance because it is related to evolutionary aspects and is successfully employed to Published: June 19, 2015 characterize and discriminate among different biological structures. Here, the fractal de- Copyright: © 2015 da Silva et al. This is an open scriptors are used to identify the species of plants based on the image of their leaves. A access article distributed under the terms of the Creative Commons Attribution License, which permits large number of samples are examined, being 606 leaf samples of 50 species from Brazilian unrestricted use, distribution, and reproduction in any flora. The results are compared to other imaging methods in the literature and demonstrate medium, provided the original author and source are that fractal descriptors are precise and reliable in the taxonomic process of plant species credited. identification. Data Availability Statement: Data are available at the Harvard Dataverse Database: https://dataverse. harvard.edu/dataset.xhtml?persistentId = doi:10. 7910/DVN/KDZVUM. Funding: NRS was supported by grant number 2011/ Introduction 21467-9, Fundação de Amparo à Pesquisa do Estado de São Paulo (http://www.bv.fapesp.br/pt/ A series of methodologies and approaches have been performed in the task of understanding bolsas/133991/reconhecimento-de-padroes- and description of the natural world surrounding us [1]. All major areas of scientific knowl- heterogeneos-e-suas-aplicacoes-em-biologia-e- edge, as geology, physics, biology and medical sciences have been searching for patterns that nanotecnologia/). JBF was supported by grant – number 2012/19143-3, Fundação de Amparo à may help in the understanding of natural phenomena [1 3]. In Biology, such aspects started in Pesquisa do Estado de São Paulo (http://www.bv. the ancient Greece, where philosophers tried to describe, identify and classify natural entities fapesp.br/pt/bolsas/140250/geometria-fractal-e- (species) based on identifiable traits [4]. The Greek philosopher Theoprasthus performed the PLOS ONE | DOI:10.1371/journal.pone.0130014 June 19, 2015 1/14 Plant Identification Using Fractal Descriptors analise-de-imagens-aplicadas-a-biologia-vegetal/). most famous case, where he proposed a classification system of plant species according to their RMK was supported by grant number 2011/23112-3, external morphology, adopting as a classifier their distinct growth forms [5]. Since these an- Fundação de Amparo à Pesquisa do Estado de São cient times, scientists have proposed a series of manners to perform classification [6–8] and to Paulo (http://www.bv.fapesp.br/pt/auxilios/46845/ anatomia-foliar-de-plantas-de-diferentes-formacoes- identify species. Yet, in plants, the older and most adopted methodology used to infer and pro- vegetacionais/). OMB was supported by grant duce classification system is the observation and description of internal and external plant number 2011/01523-1, Fundação de Amparo à traits [9, 10], associated, in recent times, with the information stored at molecular level [11]. Pesquisa do Estado de São Paulo (http://www.bv. The most common aspects used by specialists to categorize and identify species concern the fapesp.br/pt/auxilios/30465/metodos-de-visao- use of external traits of plants, in where such specialists access information stored in the form, computacional-aplicados-a-identificacao-e-analise- de-plantas/); grant number 307797/2014-7, Conselho ontogeny and number of elements forming reproductive organs (flowers) and dispersion enti- Nacional de Desenvolvimento Científico e ties (fruits) [12, 13]. The use of such elements produced both good tools to identify species and Tecnológico; and grant number 484312/2013-8, important classification systems to understand the evolution of groups of species [8, 14]. De- Conselho Nacional de Desenvolvimento Científico e spite the importance and significance of such aspects, the analysis of such structures cannot be Tecnológico. always employed, as these elements appear only in specific times of year, when plants are re- Competing Interests: The authors have declared producing or dispersing their descendants [15]. In such cases, specialists also recur and extract that no competing interests exist. information stored in vegetative parts of plants, especially the leaves, which are available for sampling throughout the year [16]. When assessing vegetative organs as the leaves, there is a chance to confound certain infor- mation provided by their morphological and anatomical analysis [17, 18], as leaves are one of the most diverse plant organs in terms of morphology and anatomy [19, 20] and such morpho- anatomical traits can vary drastically according to environmental conditions [21]. However, some studies have provided good evidence that the analysis of certain external and internal leaf structures could be of substantial information to aid species classification [22–24]. Until re- cently, information stored on vegetative traits of plants were only extracted by the human eye, which is capable of extracting low amounts of information such as shape, types, divisions, among others. Nowadays, a series of computational methodologies are available to search and extract information to discriminate plant species [21, 25], assessing properties such as texture and color, which were not possible to be inferred by conventional analysis. The use of such ap- proaches has been explored with great success, using both external [26–29] and some internal [25] aspects of leaves. Among the computational analysis of leaf internal structures, only color and texture infor- mation of photosynthetic and protection tissues have been explored with success to discrimi- nate plant species [25]. Nevertheless, leaves have a great diversity of other internal structures that can potentially store information for discrimination patterns [13, 30]. One of them is the midrib, which drastically differs between species in its shape and composition of vascular and fundamental tissues [20]. Anatomically, leaf midrib is composed by a set of highly specialized tissues (pholem and xylem) and other cells, which are normally very similar between individu- als of the same species [31], as this region is less plastic than other regions of the leaf blade, as the mesophyll for example [32]. Additionally, the midrib is considered as a stable region re- garding the conservation of its structures when submitted to the image acquisition process. The use of midrib anatomy to discriminate plant species has been recently explored as a new tool to assist plant classification [33, 34]. Such studies indicate the great potential of the compu- tational methodologies to explore the patterns of composition and arrangement of tissues and structures in the midrib, which may provide a great additional source of information to the dis- crimination of plant species. In fact, a preliminary approach using only 10 species provided evi- dence for the robustness of such kind of methodology [35]. Considering the several methodologies used to discriminate plant species, many of them successfully made use of latest and advanced methods of image analysis. Most of such methods analyze only the external shape of the leaf; although this can be sufficient in some situations, the addition of internal traits, such as that from midrib, may provide the creation of robust PLOS ONE | DOI:10.1371/journal.pone.0130014 June 19, 2015 2/14 Plant Identification Using Fractal Descriptors descriptors, able to synthesize all this informational richness in a feature vector, making the discrimination of plants a more feasible