3D modeling and reconstruction of plants and trees: A cross-cutting review across computer graphics,vision, and plant phenotyping

This paper reviews the past and current trends of three-dimensional (3D) modeling and reconstruction of plants and trees. These topics have been studied in multiple research fields, including computer vision, graphics, plant phenotyping, and forestry. This paper, therefore, provides a cross-cutting review. Representations of plant shape and structure are first summarized, where every method for plant modeling and reconstruction is based on a shape/structure representation. The methods were then categorized into 1) creating non-existent plants (modeling) and 2) creating models from real-world plants (reconstruction). This paper also discusses the limitations of current methods and possible future directions.     

Development of a plant conveyance system using an AGV and a self-designed plant-handling device: A case study of DIY plant phenotyping

Plant phenotyping technology has been actively developed in recent years, but the introduction of these technologies into the field of agronomic research has not progressed as expected, in part due to the need for flexibility and low cost. “DIY” (Do It Yourself) methodologies are an efficient way to overcome such obstacles. Devices with modular functionality are critical to DIY experimentation, allowing researchers flexibility of design. In this study, we developed a plant conveyance system using a commercial AGV (Automated Guided Vehicle) as a case study of DIY plant phenotyping. The convey module consists of two devices, a running device and a plant-handling device. The running device was developed based on a commercial AGV Kit. The plant-handling device, plant stands, and pot attachments were originally designed and fabricated by us and our associates. Software was also developed for connecting the devices and operating the system. The run route was set with magnetic tape, which can be easily changed or rerouted. Our plant delivery system was developed with low cost and having high flexibility, as a unit that can contribute to others’ DIY’ plant research efforts as well as our own. It is expected that the developed devices will contribute to diverse phenotype observations of plants in the greenhouse as well as to other important functions in plant breeding and agricultural production.     

Development of a high-throughput field phenotyping rover optimized for size-limited breeding fields as open-source hardware

Phenotyping is a critical process in plant breeding, especially when there is an increasing demand for streamlining a selection process in a breeding program. Since manual phenotyping has limited efficiency, high-throughput phenotyping methods are recently popularized owing to progress in sensor and image processing technologies. However, in a size-limited breeding field, which is common in Japan and other Asian countries, it is challenging to introduce large machinery in the field or fly unmanned aerial vehicles over the field. In this study, we developed a ground-based high-throughput field phenotyping rover that could be easily introduced to a field regardless of the scale and location of the field even without special facilities. We also made the field rover open-source hardware, making its system available to public for easy modification, so that anyone can build one for their own use at a low cost. The trial run of the field rover revealed that it allowed the collection of detailed remote-sensing images of plants and quantitative analyses based on the images. The results suggest that the field rover developed in this study could allow efficient phenotyping of plants especially in a small breeding field.     

Automatic detection of alien plant species in action camera images using the chopped picture method and the potential of citizen science

Monitoring and detection of invasive alien plant species are necessary for effective management and control measures. Although efforts have been made to detect alien trees using satellite images, the detection of alien herbaceous species has been difficult. In this study, we examined the possibility of detecting non-native plants using deep learning on images captured by two action cameras. We created a model for each camera using the chopped picture method. The models were able to detect the alien plant Solidago altissima (tall goldenrod) and obtained an average accuracy of 89%. This study proved that it is possible to automatically detect exotic plants using inexpensive action cameras through deep learning. This advancement suggests that, in the future, citizen science may be useful for conducting distribution surveys of alien plants in a wide area at a low cost.     

苹果花序几何造型及可视化研究

为了实现对苹果花及花序三维形态结构的交互设计、几何建模和真实感现实,提出了精确描述苹果花序三维形态结构的数学模型及可视化方法。通过对苹果花及花序形态结构的观测分析,分别提出了描述花柄、花托、花萼、花瓣、雄蕊和雌蕊三维形态结构的数学模型,并提取了模型的控制参数;进一步整合苹果花及花序的拓扑结构信息,实现了苹果花及花序的三维重建。为了增强花的真实感,提出了花柄、花托和花萼上绒毛的生成方法。结果表明,该方法可控性强,易于操作,可以精确重构出苹果花和花序的三维形态,实现对开花过程的可视化模拟,具有较强的真实感。     

Production of Transgenic Plants： More, Better, and Faster

Over the last two decades, transgenic plants have moved from being solely laboratory vehicles for basic research work to providing new varieties grown on large areas throughout the world. A number of plant     

OpenGL在粮仓温度场可视化中的应用

根据粮仓温度监测系统采集到的温度数据,首次在VC 6．0MFC平台上,运用3DSMAX,OpenGL图形工具包,实现了整个粮库外景三维建模以及粮仓温度场的动态三维重现。从而可直观地了解粮仓内部的温度情况。     

Technique of Surface Reconstruction for Three Dimensional Structure of Chinese Medicihnal Materials

To study the technique of surface reconstruction for Chinese medicinal materials from its cross-sectional images and to display its three dimensional structure.The pattern recognition technique is used to complete the classification and matching of various structures, then the triangle surface approximation is used to produce the 3D surface of the structure.The 3D structure is reconstructed and can be viewed by flexible way based on SGI workstation. The technique and method provided by this paper is contributive to the study and view of various structure of Chinese medicinal materials, and is available to biomedical image processing field.     

基于模板的生菜参数化几何建模方法

为了对生菜进行快速三维重构,本文将逆向工程的思想引入到生菜几何建模中来,提出了一种基于参数模板的生菜几何建模方法。借助三维扫描设备构造具有多分辨率的生菜器官模板,分析生菜植株形态结构特征,提取特征参数,进而通过形态参数对模板进行控制,并最终组装成为参数化的生菜几何模型。实验结果表明,该方法可以快速、便捷地重构出具有较高真实感的生菜几何模型,对曲面难以构造的植物器官及植株几何建模具有一定的参考意义。     

Genetics of genetic conservation. II. Sample size when collecting seed of cross-pollinating species and the information that can be obtained from the evaluation of material held in gene banks

Summary Provided that the seed collected from each plant in natural populations of a species is kept separate from that of every other, a rough estimate of the heritability of a quantitative character can be obtained from the natural progenies raised from this seed in a randomised evaluation trial; a knowledge of the reproductive biology of the species can help to make this estimate of the heritability of the character more precise.The theory employed in this evaluation procedure can be used to investigate the possibility of reducing the number of plants visited in a population, when species set all of their seed by cross-fertilisation, by taking several seeds from each. We show that it is not worth taking more than eight seeds from each plant and that, in the absence of precise information about the paternity of this seed, it might be better to follow the general recommendation of Lawrence et al. (1995), by taking only one seed from each of the 172 plants.Having investigated the minimum sample size for genetic conservation in the narrow sense, we broaden discussion to consider sample size for evaluation and regeneration. It is pointed out that it is not necessary to take more than about ten seeds from each of 20–30 randomly chosen plants in each population visited and that it is possible to reduce this number of plants if material from a number of populations is evaluated in a single trial. Finally, we draw attention to the possibility of regenerating seed from a composite population founded by raising one plant from the seed taken from each plant of the original collection, as an alternative to regenerating the seed of each accession independently from that of every other.     

基于DNA条形码技术的海南龙血树和剑叶龙血树分子鉴定

海南龙血树(Dracaena cambodiana)和剑叶龙血树(Dracaena cochinchinensis)是传统名贵中药血竭在中国的重要基源植物,但其在苗期至成株期之间难以用传统分类学进行鉴定,而DNA条形码技术为这一科学问题的解决提供了可能。本研究利用已经通过形态学鉴定的海南龙血树和剑叶龙血树叶片开发了两种龙血树的DNA条形码,发现ITS2具有较大的变异度,可与来自叶绿体的trnL-trnF作为鉴定的分子标记,并基于变异最大范围构建了分子标记的示意图。为探究龙血树的分子生态学上的进化地位,基于两种龙血树的ITS2序列与其同源的41个物种的ITS2序列构建了分子进化树,发现龙血树属植物与龙舌兰科、百合科组成分支的亲缘关系近于含有天门冬科的分支,此结果为海南龙血树和剑叶龙血树的种质资源鉴定提供了分子标记,并为龙血树属在百合纲确切分类地位的确定提供了理论和技术支持。     

矮败麦的生长发育特性及传粉特点分析

1997～ 1999年对 4 4个转育多代的矮败麦材料和父母本花期相遇程度不同的 6个群体进行了有关数据的调查、分析 ,结果表明 :(1)矮败麦的株高、抽穗期和开颖期 (分别以S1,S2 ,S3 表示 )与其姊妹散粉株的对应性状 (F1,F2 ,F3 )的关系分别是 :S1=0 5 98F1(R2 =0 4 88) ,S2 =3 5 37 0 814F2 (R2 =0 60 0 ) ,S3 =5 771 0 85 6F3 (R2 =0 5 0 0 )。另外矮败麦还表现为成穗多 ,结实率低 ,子粒饱满度和粒重不高 ,但我们所用是其后代可育株 ,故对矮败麦的选择标准要适当放宽。 (2 )矮败表的穗下节伸长 (抽穗 )速度只及其可育株的 5 8 5 % ,伸长速度无明显的高峰 ,但其伸长的持续期稍长 ,这说明矮化和发育推迟可能是同一发育现象所导致的两个结果。 (3)可育株、不育株开花、开颖之间的时间间隔和其穗子之间的空间间隔的大小对株间传粉和不育株结实都至关重要。小麦自花授粉作物的花器特点对及时高效地接受外来花粉有一定的障碍作用 ,所以人工辅助授粉可提高不育株的结实率。相比之下矮败麦更容易接受来自距离稍远一些的花粉 ,这对于进行异交传粉特别是矮秆群的传粉和杂交具有重要价值     

利用花粉管通道法将外源DNA导入水稻之研究进展

外源DNA直接导入技术以DNA片断杂交假说为理论基础，直接将目的基因或带有目的性状供体遗传物质（总DNA）通过花粉管通道法导入水稻植株，创造大量的变异材料，通过筛选获得目的性状的后代和新品种。由于简单、易行、不受受体植物种类的限制，已被越多的育种者所接受，在水稻的抗病、米质、丰产性上等各方面广为应用。介绍了外源DNA导入方法、外源基因导入类型、后代遗传变异特点及影响花粉管通道法导入的因素，优点、局限性进行了分析，同时提出了问题和展望。     

抗甘蔗花叶病毒的无标记反向重复转基因玉米

构建了无标记基因的源自玉米矮花叶病的主要病原——甘蔗花叶病毒(sugarcane mosaic virus, SCMV)复制酶基因的反向重复序列表达载体,通过农杆菌介导法以该表达载体和除草剂标记基因表达载体共转化玉米自交系综3的幼胚,用除草剂梯度筛选,获得了可育的再生株。对T₁和T₂代群体作PCR和DNA点杂交,结合温室和田间人工接种病毒进行抗病性鉴定,获得了比较稳定的对SCMV高抗的无标记转基因玉米株系。     

Research and Development a Visualization System for Medical CT Images

In order to develop a 3D visualization system for medical CT images which comply with DICOM standard, the authors study DICOM file format and methods of analyzing it, discuss the key technology of adjusting Windows Center/Windows Level of Medical CT images and 3D visualization methods, and describe the system's structure and approaches to implement every function module. Through developing 3D reconstruction software of medical CT images, surface rendering is compared with volume rendering.We succeed in implementing the visualization system for medical CT images which comply with DICOM standard. This system provides an intuitionistic way for diagnosing with medical images. The system is significant in clinical environment.     

基于数码相机的农田景物三维重建

为提出一种基于图像的农田景物三维重建方法。首先从图像文件中提取包含相机焦距等参数的EXIF信息,用以计算相机内参矩阵。根据两幅对应图像的匹配关系,求解本征矩阵并对其SVD分解获得相机外参矩阵,合并相机内外参数构成投影矩阵。其次,以SIFT匹配点的视差作为搜索范围初始限制条件,按像素邻域的SSD值匹配两幅图像中的像素,获得致密的视差图并以三维点云形式重建田块景观,最后,使用“集束调整”算法对最初三维重建结果求精,并将2维图像像素RGB值映射到三维点云上,获得最终结果。从重建效果看,方法真实再现性好,重建过程简洁,具有较高的自动化程度。     

Description and evaluation of a device for measuring vertical pulling resistance in maize (Zea mays L.)

A plant pulling device was developed to measure vertical pulling resistance in maize as evaluation method for root lodging resistance. This device allows pulling in a standardized way because it is operated by an alternating current motor with ample capacity so as not to slow down during pulling. Due to its small proportions it remains easily manoeuvrable within the experimental field. Four replicated experiments (three with single cross hybrids and one with populations) on two locations (with sandy and clay soil) were carried out to estimate various statistical and quantitative genetic parameters of pulling resistance. The number of plants pulled per plot ranged from four to seven. The mean coefficient of environmental variation was 0.14 and the heritabilities for pulling resistance in the used material, based on experimental units, ranged from 0.61 to 0.77. Selection for pulling resistance seems therefore very well possible. The correlation between the pulling values from a location with clay soil and a location with sandy soil was 0.87, so genotype × environment-interaction was small. It is argued that one obtains reliable results with the least effort by using three replications and pulling four plants per plot.Paper resulting from a study as part of the requirements for a Masters degree at the Agricultural University in Wageningen, The Netherlands.     

珙桐的群落特征及种群生态学研究进展

为了解国家一级保护植物珙桐(Davidia involucrata Baill)的生境现状,采用综合分析法对珙桐群落特征和种群生态学进行研究。结果发现：（1）珙桐群落的植物种类丰富,植物区系组成以东亚分布最多,其次是北温带,珙桐群落区系的温带成分所占比例大于热带成分,其种类组成具有亚热带向温带过渡的特征;（2）群落垂直结构可分为乔木层、灌木层、草本层和层间植物。乔木层及灌木层不发达,草本层较发达。群落根据Raunkiaer生活型谱划分以高位芽植物占优势,与其他亚热带常绿落叶林生活型谱各项比率相近似;（3）种群年龄结构及空间分布格局显示,珙桐群落未达到一个稳定状态,整个种群呈集群分布;（4）珙桐自然更新能力差,种子萌发率低,实生苗少,主要以萌芽更新为主。中国珙桐群落处于一个不稳定的濒危状态。     

植物水分含量检测综述

水分作为植物生长和发育的要素之一,其含量的检测与诊断是植物学及农业、林业等领域的重要研究课题。植物水分含量诊断主要是通过对比植物特定性状指标与正常生长环境下的指标来实现。随着植物生理、生化研究的深入以及传感、检测技术的进步,发展出众多的植物水分含量检测方法。从最初通过检测细胞液浓度来直接反映水分含量,到测量植物蒸腾速率、茎流流速、叶片水势、冠层温度、茎秆直径、特定化学物质含量等间接反映水分含量,以致现在以图像、光谱分析为基础的机器视觉等新方法成为主流。本文在充分调研国内外研究和文献的基础上,详细介绍主要的水分含量检测方法原理,分析其优缺点,试图把握植物水分检测的发展趋势和研究方向,为相关科研和应用提供有益参考。     

Effects of Plant Population Density and Intercropping with Soybean on the Fractal Dimension of Corn Plant Skeletal Images

Three-year field experiments were conducted to determine whether the temporal pattern of fractal dimension (FD) for corn ( Zea mays L.) plant structure is altered by plant population density (PPD) or intercropping with soybean [ Glycine max. (L.) Merr.], and how changes in the FD are related to changes in other canopy characteristics. Plants in monocropped corn and intercropped corn–soybean plots were randomly sampled and labelled for later identification. Corn plant structure was photographed from the side that allowed the maximum appearance of details (perpendicular to the plane of developed leaves) and from two fixed sides (side 1: parallel to the row and side 2: perpendicular to the row). Images were scanned and skeletonized, as skeletal images provide acceptable information to estimate the FD of plant structure two-dimensionally by the box-counting method. Differences in the FD estimated from images taken perpendicular to the plane of developed leaves were not significant among competition treatments. An adjustment of corn plants to treatments, by changing the orientation of the plane of developed leaves with respect to the row, was observed. Based on overall FD means, competition treatments were ranked as: high > normal ≈ intercrop ≈ low for side 1 and intercrop > low ≈ normal > high for side 2. Leaf area index (LAI) and plant height had a positive correlation with FD. In contrast, light penetration had a negative correlation with FD. In conclusion, FD provides a meaningful and effective tool for quantifying corn plant structure, measuring the structural response to cultural practices, and modelling corn plant canopies.