Verification of Geometric Model-Based Plant Phenotyping
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sensors Article Verification of Geometric Model-Based Plant Phenotyping Methods for Studies of Xerophytic Plants Paweł Drapikowski 1,*, Ewa Kazimierczak-Grygiel 2, Dominik Korecki 1 and Justyna Wiland-Szyma ´nska 2,3 1 Institute of Control and Information Engineering, Faculty of Electrical Engineering, Poznan University of Technology, Piotrowo 3a, 60-965 Poznan, Poland; [email protected] 2 Botanical Garden, Adam Mickiewicz University, D ˛abrowskiego 165, 60-594 Poznan, Poland; [email protected] (E.K.-J.); [email protected] (J.W.-S.) 3 Department of Plant Taxonomy, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland * Correspondence: [email protected]; Tel.: +48-616652874 Academic Editor: Simon X. Yang Received: 16 February 2016; Accepted: 31 May 2016; Published: 27 June 2016 Abstract: This paper presents the results of verification of certain non-contact measurement methods of plant scanning to estimate morphological parameters such as length, width, area, volume of leaves and/or stems on the basis of computer models. The best results in reproducing the shape of scanned objects up to 50 cm in height were obtained with the structured-light DAVID Laserscanner. The optimal triangle mesh resolution for scanned surfaces was determined with the measurement error taken into account. The research suggests that measuring morphological parameters from computer models can supplement or even replace phenotyping with classic methods. Calculating precise values of area and volume makes determination of the S/V (surface/volume) ratio for cacti and other succulents possible, whereas for classic methods the result is an approximation only. In addition, the possibility of scanning and measuring plant species which differ in morphology was investigated. Keywords: plant digitalization; morphological parameters; DAVID laser scanning system 1. Introduction Plant phenotyping is the comprehensive assessment of complex plant traits including their architecture. Classical methods are used to study variability, adaptation to environmental conditions and pace of growth during the vegetation period. So far, plant phenotyping has been mainly limited to crop plants or the model plant Arabidopsis thaliana (L.) Heynh [1]. In many cases, classical biometric measurement methods are sufficient. However, there are plants whose complex spatial structure and susceptibility to damage make employing conventional measurement techniques impossible or exceedingly difficult. Therefore, there is a need for new platforms and solutions that enable phenotypic evaluation of such species. In such cases, non-contact measurement techniques need to be used: preparation of a three-dimensional (3D) computer model (digitalization) and capturing plant traits based on it [1,2]. One group of plants that has not been used as an object for 3D phenotyping is xerophytes. Representatives of this remarkable group are interesting for several reasons. These plants show various morphological, anatomical and physiological adaptations to living in dry conditions and in sustaining an intensive herbivory [3–7]. They constitute the main vegetation in some desert and semi-desert Sensors 2016, 16, 924; doi:10.3390/s16070924 www.mdpi.com/journal/sensors Sensors 2016, 16, 924 2 of 14 environments and are therefore a subject of intensive ecological study [8]. Their medicinal properties Sensors 2016, 16, 924 2 of 14 are recognized by both traditional and contemporary medicine as well as veterinary science [9–12]. Xerophytesmedicinal properties are also are desirable recognized ornamental by both plantstraditional worldwide. and contemporary The demand medicine for these as well plants as is so highveterinary that their science existence [9–12]. in the wild is threatened [13]. Therefore, many xerophytes, including the whole cactiXerophytes family and are also genera desirableAloe L.ornamental and Pachypodium plants worldwide.Lindl [14 The,15 ],demand are protected for these by plants international is so law underhigh that the their Washington existence in Convention the wild is threaten (CITES)ed as [13]. well Therefore, as by national many xerophytes, laws. Therefore, including customsthe officerswhole must cacti be family able to and recognize genera Aloe them L.properly and Pachypodium to prevent Lindl illegal [14,15], traffic. are protected The diversity by international of these plants law under the Washington Convention (CITES) as well as by national laws. Therefore, customs is, however, so great that only specialists are able to recognize them and classify them accordingly. officers must be able to recognize them properly to prevent illegal traffic. The diversity of these Comprehensive virtual guides that would enable rapid and simple identification of these plants do plants is, however, so great that only specialists are able to recognize them and classify them not exist.accordingly. Comprehensive virtual guides that would enable rapid and simple identification of Climatethese plants change do not as exist. well population growth have created an urgent need for sustainable high-yield crop production.Climate change Phenotypic as well studies population of plants growth adapted have to created difficult an environmental urgent need for conditions sustainable can be helpfulhigh-yield in finding crop new production. ways for cropPhenotypic improvement studies [of16 ].plants adapted to difficult environmental Variousconditions types can be of helpful scanners in finding make non-contactnew ways for plant crop improvement digitalization [16]. possible. Most often they work by castingVarious structured types light of scanners in various make patterns non-contact onto plant the objectdigitalization and recording possible. theMost images often they (Figure work1)[ 17]. On theby basiscasting of structured disruptions light in in the various pattern patterns caused onto by the the object object’s and surface,recording a the three-dimensional images (Figure 1) point [17]. On the basis of disruptions in the pattern caused by the object’s surface, a three-dimensional cloud is determined, which is further triangulated into the form of a triangle mesh. The triangle mesh point cloud is determined, which is further triangulated into the form of a triangle mesh. The computer model is then processed to determine morphological parameters of interest. triangle mesh computer model is then processed to determine morphological parameters of interest. Figure 1. Scanning a succulent plant in the pot with the structured light-based DAVID FigureLaserscanner 1. Scanning [17]. a succulent plant in the pot with the structured light-based DAVID Laserscanner [17]. Non-contact measurements of selected characteristics are possible using the Ubiquitous Sensor Non-contactNetwork proposed measurements by Suk et al. of [18]. selected An example characteristics of image-based are possible plant usingphenotyping the Ubiquitous on a much Sensor Networklarger proposed scale wasby presented Suk et al.by [18Kircherer]. An example et al. [19], of and image-based numerous additional plant phenotyping examples can on abe much found larger [1,2,20–23]. scale was presented by Kircherer et al. [19], and numerous additional examples can be found [1,2,20– Scanning larger objects is feasible with the use of, for instance, a Kinect scanner [24]. Recently, 23]. the photogrammetric method for creating computer models has been gaining popularity. It uses a Scanningpreviously largercaptured objects set of is images. feasible There with are the no use limits of, forto the instance, size of objects: a Kinect the scanner only restriction [24]. Recently, is the the photogrammetricability to take a method photograph. for creatingProfessional computer photographic models equipment has been is not gaining required, popularity. only a digital It uses a previouslycamera is captured necessary set [25]. of These images. scanning There methods are no limits require to relatively the size oflow-cost objects: devices the only which restriction offer is the abilityacceptable to take metrological a photograph. characteristics. Professional Extensive photographic metrological equipment and usability is not descriptions required, onlyof those a digital cameradevices is necessary for plant measurement [25]. These scanninghave been published methods [2 require6,27]. Better relatively results low-cost in scanning devices plants whichof very offer acceptablecomplex metrological shapes havecharacteristics. been achieved with Extensive hand-h metrologicaleld scanners, ande.g., usabilityArtec S [28] descriptions or HandyScan of those devicesEXASCAN for plant [29]. measurement Also, triangulation have been scanners published (typically [26 ,27more]. Better accurate), results mounted in scanning on special plants of measuring arms [30,31], can be used for this purpose, e.g., Artec S and Perceptron ScanWorks V5 very complex shapes have been achieved with hand-held scanners, e.g., Artec S [28] or HandyScan with the Romer Infinite 2.0 arm. However, their prices are far higher than those of hand-held EXASCANdevices. [ 29]. Also, triangulation scanners (typically more accurate), mounted on special measuring arms [30,31], can be used for this purpose, e.g., Artec S and Perceptron ScanWorks V5 with the Romer Infinite 2.0 arm. However, their prices are far higher than those of hand-held devices. Sensors 2016, 16, 924 3 of 14 One frequently measured parameter in plant biology is S/V (surface to volume ratio). It is easy to determine it for