Rice morphogenesis and plant architecture: Measurement, specification and the reconstruction of structural development by 3D architectural modelling

Background and Aims The morphogenesis and architecture of a rice plant, Oryza sativa, are critical factors in the yield equation, but they are not well studied because of the lack of appropriate tools for 3D measurement. The architecture of rice plants is characterized by a large number of tillers and leaves. The aims of this study were to specify rice plant architecture and to find appropriate functions to represent the 3D growth across all growth stages. Methods A japonica type rice, 'Namaga', was grown in pots under outdoor conditions. A 3D digitizer was used to measure the rice plant structure at intervals from the young seedling stage to maturity. The L-system formalism was applied to create '3D virtual rice' plants, incorporating models of phenological development and leaf emergence period as a function of temperature and photoperiod, which were used to determine the timing of tiller emergence. Key Results The relationships between the nodal positions and leaf lengths, leaf angles and tiller angles were analysed and used to determine growth functions for the models. The '3D virtual rice' reproduces the structural development of isolated plants and provides a good estimation of the fillering process, and of the accumulation of leaves. Conclusions The results indicated that the '3D virtual rice' has a possibility to demonstrate the differences in the structure and development between cultivars and under different environmental conditions. Future work, necessary to reflect both cultivar and environmental effects on the model performance, and to link with physiological models, is proposed in the discussion.

An analytical tool that quantifies cellular morphology changes from three-dimensional fluorescence images

The most common software analysis tools available for measuring fluorescence images are for two-dimensional (2D) data that rely on manual settings for inclusion and exclusion of data points, and computer-aided pattern recognition to support the interpretation and findings of the analysis. It has become increasingly important to be able to measure fluorescence images constructed from three-dimensional (3D) datasets in order to be able to capture the complexity of cellular dynamics and understand the basis of cellular plasticity within biological systems. Sophisticated microscopy instruments have permitted the visualization of 3D fluorescence images through the acquisition of multispectral fluorescence images and powerful analytical software that reconstructs the images from confocal stacks that then provide a 3D representation of the collected 2D images. Advanced design-based stereology methods have progressed from the approximation and assumptions of the original model-based stereology(1) even in complex tissue sections(2). Despite these scientific advances in microscopy, a need remains for an automated analytic method that fully exploits the intrinsic 3D data to allow for the analysis and quantification of the complex changes in cell morphology, protein localization and receptor trafficking. Current techniques available to quantify fluorescence images include Meta-Morph (Molecular Devices, Sunnyvale, CA) and Image J (NIH) which provide manual analysis. Imaris (Andor Technology, Belfast, Northern Ireland) software provides the feature MeasurementPro, which allows the manual creation of measurement points that can be placed in a volume image or drawn on a series of 2D slices to create a 3D object. This method is useful for single-click point measurements to measure a line distance between two objects or to create a polygon that encloses a region of interest, but it is difficult to apply to complex cellular network structures. Filament Tracer (Andor) allows automatic detection of the 3D neuronal filament-like however, this module has been developed to measure defined structures such as neurons, which are comprised of dendrites, axons and spines (tree-like structure). This module has been ingeniously utilized to make morphological measurements to non-neuronal cells(3), however, the output data provide information of an extended cellular network by using a software that depends on a defined cell shape rather than being an amorphous-shaped cellular model. To overcome the issue of analyzing amorphous-shaped cells and making the software more suitable to a biological application, Imaris developed Imaris Cell. This was a scientific project with the Eidgenössische Technische Hochschule, which has been developed to calculate the relationship between cells and organelles. While the software enables the detection of biological constraints, by forcing one nucleus per cell and using cell membranes to segment cells, it cannot be utilized to analyze fluorescence data that are not continuous because ideally it builds cell surface without void spaces. To our knowledge, at present no user-modifiable automated approach that provides morphometric information from 3D fluorescence images has been developed that achieves cellular spatial information of an undefined shape (Figure 1). We have developed an analytical platform using the Imaris core software module and Imaris XT interfaced to MATLAB (Mat Works, Inc.). These tools allow the 3D measurement of cells without a pre-defined shape and with inconsistent fluorescence network components. Furthermore, this method will allow researchers who have extended expertise in biological systems, but not familiarity to computer applications, to perform quantification of morphological changes in cell dynamics.

基于分支设置的质量导引相位展开算法

二维相位展开方法是近年来较为活跃、引起关注的一个研究课题，它在许多测量应用中有着重要的作用。尽管掩膜阻断算法在多个领域都有成功应用实例，该算法存在着固有的缺陷。为了克服掩膜阻断算法的缺陷，综合分支阻断方法和质量导引方法的优点，提出一种基于分支设置的质量导引相位展开新算法。它先以一个初始质量图来引导分支的设置，然后把分支对应的相位质量设置为最低，从而产生一个新的质量图，最后按新质量图来引导相位展开，并使用几个包裹相位图来验证此方法的有效性。计算机模拟相位图和实际相位图的相位展开结果表明，在存在复杂轮廓不连续

PSD空间定位的非线性误差补偿模型及归一化

PSD是一种高分辨率、实时性好的光电位置敏感器件,因而具有广泛应用的前景.但在光照度变化条件下,输出信号存在非线性飘移,因而影响了作为位置检测传感器的检测精度,尤其在3D测量时适用性受到了限制.针对这个问题,提出了一种PSD位置传感器的非线性误差补偿方法.该方法针对目标的空间距离变化所产生的PSD输出非线性飘移,采用归一化模型进行误差修正,很大程度上改进了PSD的输出一致性,使基于PSD的3D测量系统性能得以提高.

Fliesslochformen und Gewindefurchen in dünne Bleche und Rohre aus Kupfer und Kupferlegierungen

This thesis in Thermal Flow Drilling and Flowtap in thin metal sheet and pipes of copper and copper alloys had as objectives to know the comportment of copper and copper alloys sheet metal during the Thermal Flow Drill processes with normal tools, to know the best Speed and Feed machine data for the best bushing quality, to known the best Speed for Form Tapping processes and to know the best bush long in pure copper pipes for water solar interchange equipment. Thermal Flow Drilling (TFD) and Form Tapping (FT) is one of the research lines of the Institute of Production and Logistics (IPL) at University of Kassel. At December 1995, a work meeting of IPL, Santa Catarina University, Brazil, Buenos Aires University, Argentine, Tarapacá University (UTA), Chile members and the CEO of Flowdrill B.V. was held in Brazil. The group decided that the Manufacturing Laboratory (ML) of UTA would work with pure copper and brass alloys sheet metal and pure copper pipes in order to develop a water interchange solar heater. The Flowdrill BV Company sent tools to Tarapacá University in 1996. In 1999 IPL and the ML carried out an ALECHILE research project promoted by the DAAD and CONICyT in copper sheet metal and copper pipes and sheet metal a-brass alloys. The normal tools are lobed, conical tungsten carbide tool. When rotated at high speed and pressed with high axial force into sheet metal or thin walled tube generated heat softens the metal and allows the drill to feed forward produce a hole and simultaneously form a bushing from the displacement material. In the market exist many features but in this thesis is used short and longs normal tools of TFD. For reach the objectives it was takes as references four qualities of the frayed end bushing, where the best one is the quality class I. It was used pure copper and a-brass alloys sheet metals, with different thickness. It was used different TFD drills diameter for four thread type, from M-5 to M10. Similar to the Aluminium sheet metals studies it was used the predrilling processes with HSS drills around 30% of the TFD diameter (1,5 – 3,0 mm D). In the next step is used only 2,0 mm thick metal sheet, and 9,2 mm TFD diameter for M-10 thread. For the case of pure commercial copper pipes is used for ¾” inch diameter and 12, 8 mm (3/8”) TFD drill for holes for 3/8” pipes and different normal HSS drills for predrilling processes. The chemical sheet metal characteristics were takes as reference for the material behaviour. The Chilean pure copper have 99,35% of Cu and 0,163% of Zinc and the Chilean a-brass alloys have 75,6% of Cu and 24,0% of Zinc. It is used two German a-brass alloys; Nº1 have 61,6% of Cu, 36,03 % of Zinc and 2,2% of Pb and the German a-brass alloys Nº2 have 63,1% of Cu, 36,7% of Zinc and 0% of Pb. The equipments used were a HAAS CNC milling machine centre, a Kistler dynamometer, PC Pentium II, Acquisition card, TESTPOINT and XAct software, 3D measurement machine, micro hardness, universal test machine, and metallographic microscope. During the test is obtained the feed force and momentum curves that shows the material behaviour with TFD processes. In general it is take three phases. It was possible obtain the best machining data for the different sheet of copper and a-brass alloys thick of Chilean materials and bush quality class I. In the case of a-brass alloys, the chemical components and the TFD processes temperature have big influence. The temperature reach to 400º Celsius during the TFD processes and the a-brass alloys have some percents of Zinc the bush quality is class I. But when the a-brass alloys have some percents of Lead who have 200º C melting point is not possible to obtain a bush, because the Lead gasify and the metallographic net broke. During the TFD processes the recrystallization structures occur around the Copper and a-brass alloy bush, who gives more hardness in these zones. When the threads were produce with Form Tapping processes with Flowtap tools, this hardness amount gives a high limit load of the thread when hey are tested in a special support that was developed for it. For eliminated the predrilling processes with normal HSS drills it was developed a compound tool. With this new tool it was possible obtain the best machining data for quality class I bush. For the copper pipes it is made bush without predrilling and the quality class IV was obtained. When it is was used predrilling processes, quality classes I bush were obtained. Then with different HSS drill diameter were obtained different long bush, where were soldering with four types soldering materials between pipes with 3/8” in a big one as ¾”. Those soldering unions were tested by traction test and all the 3/8” pipes broken, and the soldering zone doesn’t have any problem. Finally were developed different solar water interchange heaters and tested. As conclusions, the present Thesis shows that the Thermal Flow Drilling in thinner metal sheets of cooper and cooper alloys needs a predrilling process for frayed end quality class I bushings, similar to thinner sheets of aluminium bushes. The compound tool developed could obtain quality class I bushings and excludes predrilling processes. The bush recrystalization, product of the friction between the tool and the material, the hardness grows and it is advantageous for the Form Tapping. The methodology developed for commercial copper pipes permits to built water solar interchange heaters.

An approach to coded structured light to obtain three dimensional information

The human visual ability to perceive depth looks like a puzzle. We perceive three-dimensional spatial information quickly and efficiently by using the binocular stereopsis of our eyes and, what is mote important the learning of the most common objects which we achieved through living. Nowadays, modelling the behaviour of our brain is a fiction, that is why the huge problem of 3D perception and further, interpretation is split into a sequence of easier problems. A lot of research is involved in robot vision in order to obtain 3D information of the surrounded scene. Most of this research is based on modelling the stereopsis of humans by using two cameras as if they were two eyes. This method is known as stereo vision and has been widely studied in the past and is being studied at present, and a lot of work will be surely done in the future. This fact allows us to affirm that this topic is one of the most interesting ones in computer vision. The stereo vision principle is based on obtaining the three dimensional position of an object point from the position of its projective points in both camera image planes. However, before inferring 3D information, the mathematical models of both cameras have to be known. This step is known as camera calibration and is broadly describes in the thesis. Perhaps the most important problem in stereo vision is the determination of the pair of homologue points in the two images, known as the correspondence problem, and it is also one of the most difficult problems to be solved which is currently investigated by a lot of researchers. The epipolar geometry allows us to reduce the correspondence problem. An approach to the epipolar geometry is describes in the thesis. Nevertheless, it does not solve it at all as a lot of considerations have to be taken into account. As an example we have to consider points without correspondence due to a surface occlusion or simply due to a projection out of the camera scope. The interest of the thesis is focused on structured light which has been considered as one of the most frequently used techniques in order to reduce the problems related lo stereo vision. Structured light is based on the relationship between a projected light pattern its projection and an image sensor. The deformations between the pattern projected into the scene and the one captured by the camera, permits to obtain three dimensional information of the illuminated scene. This technique has been widely used in such applications as: 3D object reconstruction, robot navigation, quality control, and so on. Although the projection of regular patterns solve the problem of points without match, it does not solve the problem of multiple matching, which leads us to use hard computing algorithms in order to search the correct matches. In recent years, another structured light technique has increased in importance. This technique is based on the codification of the light projected on the scene in order to be used as a tool to obtain an unique match. Each token of light is imaged by the camera, we have to read the label (decode the pattern) in order to solve the correspondence problem. The advantages and disadvantages of stereo vision against structured light and a survey on coded structured light are related and discussed. The work carried out in the frame of this thesis has permitted to present a new coded structured light pattern which solves the correspondence problem uniquely and robust. Unique, as each token of light is coded by a different word which removes the problem of multiple matching. Robust, since the pattern has been coded using the position of each token of light with respect to both co-ordinate axis. Algorithms and experimental results are included in the thesis. The reader can see examples 3D measurement of static objects, and the more complicated measurement of moving objects. The technique can be used in both cases as the pattern is coded by a single projection shot. Then it can be used in several applications of robot vision. Our interest is focused on the mathematical study of the camera and pattern projector models. We are also interested in how these models can be obtained by calibration, and how they can be used to obtained three dimensional information from two correspondence points. Furthermore, we have studied structured light and coded structured light, and we have presented a new coded structured light pattern. However, in this thesis we started from the assumption that the correspondence points could be well-segmented from the captured image. Computer vision constitutes a huge problem and a lot of work is being done at all levels of human vision modelling, starting from a)image acquisition; b) further image enhancement, filtering and processing, c) image segmentation which involves thresholding, thinning, contour detection, texture and colour analysis, and so on. The interest of this thesis starts in the next step, usually known as depth perception or 3D measurement.

Budowa, asymetria i dymorfizm płciowy stawu ramiennego w populacji średniowiecznej i współczesnej

Wydział Biologii: Instytut Antropologii

Prostate gland and extra-capsular tissue 3D reconstruction and measurement

Currently there are little objective parameters that can quantify the success of one form of prostate surgical removal over another. Accordingly, at Old Dominion University (ODU) we have been developing a process resulting in the use of software algorithms to assess the coverage and depth of extra-capsular soft tissue removed with the prostate by the various surgical approaches. Parameters such as the percent of capsule that is bare of soft tissue and where present the depth and extent of coverage have been assessed. First, visualization methods and tools are developed for images of prostate slices that are provided to ODU by the Pathology Department at Eastern Virginia Medical School (EVMS). The visualization tools interpolate and present 3D models of the prostates. Measurement algorithms are then applied to determine statistics about extra-capsular tissue coverage. This paper addresses the modeling, visualization, and analysis of prostate gland tissue to aid in quantifying prostate surgery success. Particular attention is directed towards the accuracy of these measurements and is addressed in the analysis discussions.