An accurate and effective FMM-based approach for freehand 3D ultrasound reconstruction

Freehand three-dimensional ultrasound imaging is a highly attractive research area because it is capable of volumetric visualization and analysis of tissues and organs. The reconstruction algorithm plays a key role to the construction of three-dimensional ultrasound volume data with higher image quality and faster reconstruction speed. However, a systematic approach to such problem is still missing. A new fast marching method (FMM) for three-dimensional ultrasound volume reconstruction using the tracked and hand-held probe is proposed in this paper. Our reconstruction approach consists of two stages: bin-filling stage and hole-filling stage. Each pixel in the B-scan images is traversed and its intensity value is assigned to its nearest voxel in the bin-filling stage. For the efficient and accurate reconstruction, we present a new hole-filling algorithm based on the fast marching method. Our algorithm advances the interpolation boundary along its normal direction and fills the area closest to known voxel points in first, which ensure that the structural details of image can be preserved. Experimental results on both ultrasonic abdominal phantom and in vivo urinary bladder of human subject and comparisons with some popular algorithms are used to demonstrate its improvement in both reconstruction accuracy and efficiency.     

三维几何形态测量方法在石制品分析中的应用

几何形态测量方法是生物学研究中用于形态特征分析和形态比较研究的一种常用方法。其核心思想是利用空间坐标点获取研究对象的形态数据,再通过坐标数据的多元统计分析,定量探讨研究对象的形态特征及影响其形态变异的因素。近年来,随着三维扫描技术的广泛应用以及对于石制品形态特征量化分析要求的提高,基于三维模型的几何形态测量方法开始出现在相关的旧石器考古研究中。本文首先对三维几何形态测量分析方法及其在石制品研究中的应用情况进行介绍,随后具体阐述了该方法的分析流程。为便于国内学者更好地了解这一方法,本文进一步以广西百色盆地南坡山遗址发现的手斧为例,利用三维几何形态测量方法对这些手斧的几何形态特征进行了初步探讨。三维几何形态测量方法为石制品形态研究提供了新思路和新视角,有望成为今后中国旧石器考古研究中一个重要的发展方向。     

3D representation and analysis of enthesis morphology

This comparison of methods for assessing the development of muscle insertion sites, or entheses, suggests that three‐dimensional (3D) quantification of enthesis morphology can produce a picture of habitual muscle use patterns in a past population that is similar to one produced by ordinal scores for describing enthesis morphology. Upper limb skeletal elements (humeri, radii, and ulnae) from a sample of 24 middle‐aged adult males from the Pottery Mound site in New Mexico were analyzed for both fibrous and fibrocartilaginous enthesis development with three different methods: ordinal scores, two‐dimensional (2D) area measurements, and 3D surface areas. The methods were compared using tests for asymmetry and correlations among variables in each quantitative data set. 2D representations of enthesis area did not agree as closely as ordinal scores and 3D surface areas did regarding which entheses were significantly asymmetrical. There was significant correlation between 3D and 2D data, but correlation coefficients were not consistently high. Intraobserver error was also assessed for the 3D method. Cronbach's alpha values fell between 0.68 and 0.73, and error rates for all entheses fell between 10% and 15%. Marginally acceptable intraobserver error and the analytic versatility of 3D images encourage further investigation of using 3D scanning technology for quantifying enthesis development. Am J Phys Anthropol 152:417–424, 2013. © 2013 Wiley Periodicals, Inc.     

Cross-sectional interpolation of annual rings within a 3D root model

Ring width of a given year can be highly variable throughout the cross section of a stem. This is especially true for roots. Therefore, the entire circumference of tree rings is often needed for studies focusing on specific reactions of individual trees on certain environmental conditions. Also, ring reconstructions are of interest for biomass calculations estimated by the cross-sectional area. The aim of the study is thus to reconstruct tree rings of cross sections within a 3D root-surface model, which will be the basis for an upcoming 3D root-development model. A FARO ScanArm was used for the acquisition of the 3D root structure (Technologies Inc., 2010). Afterwards ring-width data was measured along 4 radii per cross section and the resulting ring boundaries were integrated into the 3D root model. A weighted interpolation algorithm was used to reconstruct entire ring-width profiles of the cross sections. The algorithm considered the ring-width variations of the adjacent radii as well as the outer shape of the cross section. Hence, the intention was to estimate ring width around the root circumference using ring widths measured along 4 radii and the surface dimensions of roots. Interpolated ring-width data was compared to the measured tree-ring data as a control for the developed interpolation algorithm. Comparisons between modelled and empirical values showed a mean absolute error of about 0.06 mm deviation, and with a few exceptions the growth patterns could be accurately simulated. This has permitted additional radii measurements to be replaced by model interpolations.     

大鼠肠道系统的高分辨解剖数据集及三维模型的构建

利用冰冻铣切技术获取的大鼠腹部的断面图像,构建了大鼠肠道系统的高分辨解剖数据集及三维模型,该数据集及模型具有信息丰富等特点.本工作为开展高等动物肠道系统功能与结构关系的"定量研究及系统整合"提供了基础.     

Evaluation of a no-reference image quality metric for projection X-ray imaging using a 3D printed patient-specific phantom

PurposeFeasability of a no-reference image quality metric was assessed on patient-like images using a patient-specific phantom simulating a frame of a coronary angiogram.MethodsOne background and one contrast-filled frame of a coronary angiogram, acquired using a clinical imaging protocol, were selected from a Philips Integris Allura FD (Philips Healthcare, Best, The Netherlands). The background frame’s pixels were extruded to a thickness proportional to their grey value. One phantom was 3D printed using composite 80% bronze filament (max. thickness of 5.1 mm), the other was a custom PMMA cast (max thickness of 8.5 cm). A vessel mold was created from the contrast-filled frame and injected with a solution of 320 mg I/ml contrast fluid (75%), water and gelatin. Still X-ray frames of the vessel mold + background phantom + 16 cm PMMA were acquired at manually selected different exposure settings using a Philips Azurion (Philips Healthcare, Best, The Netherlands) in User Quality Control Mode and were exported as RAW images. The signal-difference-to-noise-ratio-squared (SDNR²) and a spatial-domain-equivalent of the noise equivalent quanta (NEQ_SDE) were calculated. The Spearman’s correlation of the latter parameters with a no-reference perceptual image quality metric (NIQE) was investigated.ResultsThe bronze phantom showed better resemblance to the original patient frame selected from a coronary angiogram of an actual patient, with better contrast and less blur than the PMMA phantom. Both phantoms were imaged using a comparable imaging protocol to the one used to acquire the original frame. The bronze phantom was hence used together with the vessel mold for image quality measurements on the 165 still phantom frames. A strong correlation was noted between NEQ_SDE and NIQE (SROCC = –0.99, p < 0.0005) and between SDNR² and NIQE (SROCC = –0.97, p < 0.0005).ConclusionUsing a cost-effective and easy to realize patient-specific phantom we were able to generate patient-like X-ray frames. NIQE as a no-reference image quality model has the potential to predict physical image quality from patient images.     

Development of a 3D optical scanner for evaluating patient-specific dose distributions

PurposeThis paper describes the hardware and software characteristics of a 3D optical scanner (P3DS) developed in-house. The P3DS consists of an LED light source, diffuse screen, step motor, CCD camera, and scanner management software with 3D reconstructed software.Materials and methodWe performed optical simulation, 2D and 3D reconstruction image testing, and pre-clinical testing for the P3DS. We developed the optical scanner with three key characteristics in mind. First, we developed a continuous scanning method to expand possible clinical applications. Second, we manufactured a collimator to improve image quality by reducing scattering from the light source. Third, we developed an optical scanner with changeable camera positioning to enable acquisition of optimal images according to the size of the gel dosimeter.ResultsWe confirmed ray-tracing in P3DS with optic simulation and found that 2D projection and 3D reconstructed images were qualitatively similar to the phantom images. For pre-clinical tests, the dose distribution and profile showed good agreement among RTP, optical CT, and external beam radiotherapy film data for the axial and coronal views. The P3DS has shown that it can scan and reconstruct for evaluation of the gel dosimeter within 1 min. We confirmed that the P3DS system is a useful tool for the measurement of 3D dose distributions for 3D radiation therapy QA. Further experiments are needed to investigate quantitative analysis for 3D dose distribution.     

3D Modelling of Biological Systems for Biomimetics

1　IntroductionBasedonthereviewofthepreviousworkof 3Dgeometricalmodellingtechniquesandsystemsdevelopedforindustrial,medicalandanimationapplications,thispaperdiscussestheproblemsassociatedwiththeexist ingtechniquesandsystems ,especiallywhenappliedto3Dmodellingof plants ,insectsandanimalsforbiomimeticsresearchanddevelopment .Then ,paperproposessomeareasofresearchinterestsin 3Dmod ellingofplants ,insectsandanimalsforBiomimetics .Toavoidtherepeating ,inthispaper ,biologicalobjectswillbeusedtorep…     

Improving the spatial orientation of human teeth using a virtual 3D approach

Since teeth are resistant to decomposition processes, they provide important and at times unique sources of information about fossil humans. Fortunately, dental remains reflect significant evolutionary changes. These changes make a very important and often exclusive contribution to the definition of new taxa or the attribution of fossil specimens to existing taxa.The traditional approach to dental morphometric analyses usually focuses on the recording of several measures of the tooth with calipers, especially the two basic crown diameters (buccolingual and mesiodistal). However, since these measures do not adequately represent the complex morphology of the tooth, 2D images and 3D digital models of dental morphology have been used. For both types of analysis, the possibility of correctly comparing homologous teeth depends on the adoption of a common orientation system. The lack of such a system makes it difficult to compare the results of different studies.Here we describe a new method for orienting teeth specifically devised for the upper and lower first molar (M1). Samples of unworn maxillary (n = 15) and mandibular (n = 15) first molars of modern humans were scanned with a Roland Picza 3D digitizer. The 3D virtual models were used to compare our new orientation method with those proposed in the literature. The new orientation system, which meets a geometric criterion, is based on three points identified on the cervical line and ensures acceptable repeatability of the spatial positioning and orientation independent of the shape and wear of the first molar under investigation. This orientation system is a first step toward the creation of a virtual set of hominid and fossil human first molars, which will allow us to make comparisons via a sophisticated and noninvasive approach. This pilot study also provides guidelines to extend the new methodology to the other types of teeth.     

Segmentation of 3D tubular objects with adaptive front propagation and minimal tree extraction for 3D medical imaging

We present a new fast approach for segmentation of thin branching structures, like vascular trees, based on Fast-Marching (FM) and Level Set (LS) methods. FM allows segmentation of tubular structures by inflating a “long balloon” from a user given single point. However, when the tubular shape is rather long, the front propagation may blow up through the boundary of the desired shape close to the starting point. Our contribution is focused on a method to propagate only the useful part of the front while freezing the rest of it. We demonstrate its ability to segment quickly and accurately tubular and tree-like structures. We also develop a useful stopping criterion for the causal front propagation. We finally derive an efficient algorithm for extracting an underlying 1D skeleton of the branching objects, with minimal path techniques. Each branch being represented by its centerline, we automatically detect the bifurcations, leading to the “Minimal Tree” representation. This so-called “Minimal Tree” is very useful for visualization and quantification of the pathologies in our anatomical data sets. We illustrate our algorithms by applying it to several arteries datasets.     

3D-DIASemb: a computer-assisted system for reconstructing and motion analyzing in 4D every cell and nucleus in a developing embryo

A computer-assisted three-dimensional (3D) system, 3D-DIASemb, has been developed that allows reconstruction and motion analysis of cells and nuclei in a developing embryo. In the system, 75 optical sections through a live embryo are collected in the z axis by using differential interference contrast microscopy. Optical sections for one reconstruction are collected in a 2.5-s period, and this process is repeated every 5 s. The outer perimeter and nuclear perimeter of each cell in the embryo are outlined in each optical section, converted into beta-spline models, and then used to construct 3D faceted images of the surface and nucleus of every cell in the developing embryo. Because all individual components of the embryo (i.e., each cell surface and each nuclear surface) are individually reconstructed, 3D-DIASemb allows isolation and analysis of (1) all or select nuclei in the absence of cell surfaces, (2) any single cell lineage, and (3) any single nuclear lineage through embryogenesis. Because all reconstructions represent mathematical models, 3D-DIASemb computes over 100 motility and dynamic morphology parameters for every cell, nucleus, or group of cells in the developing embryo at time intervals as short as 5 s. Finally, 3D-DIASemb reconstructs and motion analyzes cytoplasmic flow through the generation and analysis of "vector flow plots." To demonstrate the unique capabilities of this new technology, a Caenorhabditis elegans embryo is reconstructed and motion analyzed through the 28-cell stage. Although 3D-DIASemb was developed by using the C. elegans embryo as the experimental model, it can be applied to other embryonic systems. 3D-DIASemb therefore provides a new method for reconstructing and motion analyzing in 4D every cell and nucleus in a live, developing embryo, and should provide a powerful tool for assessing the effects of drugs, environmental perturbations, and mutations on the cellular and nuclear dynamics accompanying embryogenesis.     

The classic receptor for 1alpha,25-dihydroxy vitamin D3 is required for non-genomic actions of 1alpha,25-dihydroxy vitamin D3 in osteosarcoma cells

1alpha,25-dihydroxy vitamin D3 has a major role in the regulation of the bone metabolism as it promotes the expression of key bone-related proteins in osteoblastic cells. In recent years it has become increasingly evident that in addition to its well-established genomic actions, 1alpha,25-dihydroxy vitamin D3 induces non-genomic responses by acting through a specific plasma membrane-associated receptor. Results from several groups suggest that the classical nuclear 1alpha,25-dihydroxy vitamin D3 receptor (VDR) is also responsible for these non-genomic actions of 1alpha,25-dihydroxy vitamin D3. Here, we have used siRNA to suppress the expression of VDR in osteoblastic cells and assessed the role of VDR in the non-genomic response to 1alpha,25-dihydroxy vitamin D3. We report that expression of the classic VDR in osteoblasts is required to generate a rapid 1alpha,25-dihydroxy vitamin D3-mediated increase in the intracellular Ca(2+) concentration, a hallmark of the non-genomic actions of 1alpha,25-dihydroxy vitamin D3 in these cells.     

Evolving technologies for growing,imaging and analyzing 3D root system architecture of crop plants

A plant's ability to maintain or improve its yield under limiting conditions,such as nutrient de ficiency or drought,can be strongly in fluenced by root system architecture(RSA),the three-dimensional distribution of the different root types in the soil. The ability to image,track and quantify these root system attributes in a dynamic fashion is a useful tool in assessing desirable genetic and physiological root traits. Recent advances in imaging technology and phenotyping software have resulted in substantive progress in describing and quantifying RSA. We have designed a hydroponic growth system which retains the three-dimensional RSA of the plant root system,while allowing for aeration,solution replenishment and the imposition of nutrient treatments,as well as high-quality imaging of the root system. The simplicity and flexibility of the system allows for modi fications tailored to the RSA of different crop species and improved throughput. This paper details the recent improvements and innovations in our root growth and imaging system which allows for greater image sensitivity(detection of fine roots and other root details),higher ef ficiency,and a broad array of growing conditions for plants that more closely mimic those found under field conditions.     

3-D printing provides a novel approach for standardization and reproducibility of freezing devices

Cryopreservation has become an important and accepted tool for long-term germplasm conservation of animals and plants. To protect genetic resources, repositories have been developed with national and international cooperation. For a repository to be effective, the genetic material submitted must be of good quality and comparable to other submissions. However, due to a variety of reasons, including constraints in knowledge and available resources, cryopreservation methods for aquatic species vary widely across user groups which reduces reproducibility and weakens quality control. Herein we describe a standardizable freezing device produced using 3-dimensional (3-D) printing and introduce the concept of network sharing to achieve aggregate high-throughput cryopreservation for aquatic species. The objectives were to: 1) adapt widely available polystyrene foam products that would be inexpensive, portable, and provide adequate work space; 2) develop a design suitable for 3-D printing that could provide multiple configurations, be inexpensive, and easy to use, and 3) evaluate various configurations to attain freezing rates suitable for various common cryopreservation containers. Through this approach, identical components can be accessed globally, and we demonstrated that 3-D printers can be used to fabricate parts for standardizable freezing devices yielding relevant and reproducible cooling rates across users. With standardized devices for freezing, methods and samples can harmonize into an aggregated high-throughput pathway not currently available for aquatic species repository development.     

3D ultrasound imaging of the human corpus luteum

The aim of this article was to present the extent to which the state-of-the art ultrasonographic imaging can be used to visualize the features of the human corpus luteum (CL). In the late 1970s, the first ultrasonographic images of human CLs were published. The advent of transvaginal, high-resolution transducers has greatly improved the quality of imaging as did the subsequent introduction of color Doppler and 3D ultrasonography. In the present technical note, the examples of the various technical and imaging modalities used to examine the human CLs are shown. CL is a short-lived structure with a highly variable morphological appearance and the 3D ultrasonographic technique is an ideal tool to perform standardized measurements on the CL. The introduction of new imaging techniques in clinical reproductive medicine can only be successful if operators are properly trained.     

A new bioinformatic approach to detect common 3D sites in protein structures

An innovative bioinformatic method has been designed and implemented to detect similar three-dimensional (3D) sites in proteins. This approach allows the comparison of protein structures or substructures and detects local spatial similarities: this method is completely independent from the amino acid sequence and from the backbone structure. In contrast to already existing tools, the basis for this method is a representation of the protein structure by a set of stereochemical groups that are defined independently from the notion of amino acid. An efficient heuristic for finding similarities that uses graphs of triangles of chemical groups to represent the protein structures has been developed. The implementation of this heuristic constitutes a software named SuMo (Surfing the Molecules), which allows the dynamic definition of chemical groups, the selection of sites in the proteins, and the management and screening of databases. To show the relevance of this approach, we focused on two extreme examples illustrating convergent and divergent evolution. In two unrelated serine proteases, SuMo detects one common site, which corresponds to the catalytic triad. In the legume lectins family composed of >100 structures that share similar sequences and folds but may have lost their ability to bind a carbohydrate molecule, SuMo discriminates between functional and non-functional lectins with a selectivity of 96%. The time needed for searching a given site in a protein structure is typically 0.1 s on a PIII 800MHz/Linux computer; thus, in further studies, SuMo will be used to screen the PDB.     

3D imaging of diatoms with ion-abrasion scanning electron microscopy

Ion-abrasion scanning electron microscopy (IASEM) takes advantage of focused ion beams to abrade thin sections from the surface of bulk specimens, coupled with SEM to image the surface of each section, enabling 3D reconstructions of subcellular architecture at 30 nm resolution. Here, we report the first application of IASEM for imaging a biomineralizing organism, the marine diatom Thalassiosira pseudonana. Diatoms have highly patterned silica-based cell wall structures that are unique models for the study and application of directed nanomaterials synthesis by biological systems. Our study provides new insights into the architecture and assembly principles of both the “hard” (siliceous) and “soft” (organic) components of the cell. From 3D reconstructions of developmentally synchronized diatoms captured at different stages, we show that both micro- and nanoscale siliceous structures can be visualized at specific stages in their formation. We show that not only are structures visualized in a whole-cell context, but demonstrate that fragile, early-stage structures are visible, and that this can be combined with elemental mapping in the exposed slice. We demonstrate that the 3D architectures of silica structures, and the cellular components that mediate their creation and positioning can be visualized simultaneously, providing new opportunities to study and manipulate mineral nanostructures in a genetically tractable system.     

A novel identification approach for discovery of 5-HydroxyTriptamine 2A antagonists: combination of 2D/3D similarity screening,molecular docking and molecular dynamics

5-HydroxyTriptamine 2A antagonists are potential targets for treatment of various cerebrovascular and cardiovascular disorders. In this study, we have developed and performed a unique screening pipeline for filtering ZINC database compounds on the basis of similarities to known antagonists to determine novel small molecule antagonists of 5-HydroxyTriptamine 2A. The screening pipeline is based on 2D similarity, 3D dissimilarity and a combination of 2D/3D similarity. The shortlisted compounds were docked to a 5-HydroxyTriptamine 2A homology-based model, and complexes with low binding energies (287 complexes) were selected for molecular dynamics (MD) simulations in a lipid bilayer. The MD simulations of the shortlisted compounds in complex with 5-HydroxyTriptamine 2A confirmed the stability of the complexes and revealed novel interaction insights. The receptor residues S239, N343, S242, S159, Y370 and D155 predominantly participate in hydrogen bonding. π–π stacking is observed in F339, F340, F234, W151 and W336, whereas hydrophobic interactions are observed amongst V156, F339, F234, V362, V366, F340, V235, I152 and W151. The known and potential antagonists shortlisted by us have similar overlapping molecular interaction patterns. The 287 potential 5-HydroxyTriptamine 2A antagonists may be experimentally verified.     

Development and validation of a generic 3D model of the distal femur

The development and validation of a virtual generic 3D model of the distal femur using computer graphical methods is presented. The synthesis of the generic model requires the following steps: acquisition of bony 3D morphology using standard computed tomography (CT) imaging; alignment of 3D models reconstructed from CT images with a common coordinate system; computer graphical sectioning of the models; extraction of bone contours from the image sections; combining and averaging of extracted contours; and 3D reconstruction of the averaged contours.

The generic models reconstructed from the averaged contours of six cadaver femora were validated by comparing their surface geometry on a point to point basis with that of the CT reconstructed reference models. The mean errors ranged from 0.99 to 2.5 mm and were in agreement with the qualitative assessment of the models.