3D reconstruction of the ribs from lateral and frontal X-rays in comparison to 3D CT-scan reconstruction

Subject-specific three-dimensional (3D) reconstructions of the ribs can be obtained from biplanar X-rays. The goal of this study was to evaluate the accuracy and the inter-observer reproducibility of this technique in comparison to CT-scan reconstructions. CT scans and biplanar X-rays were obtained from 50 ribs (from three cadaveric rib cages). Three experienced experimenters reconstructed each rib from biplanar X-rays. Morphometric parameters were then computed from the rib midlines. Differences were computed between parameters obtained from the 3D reconstructions based on biplanar X-rays and from CT scans. The accuracy was computed as the mean of this difference for the 50 ribs from all three experimenters. The inter-observer variability was assessed using the coefficient of variation (CV) between the three observers. The CT-scan reconstructions were considered to be the gold standard in spite of their limitations for rib reconstructions. According to the different linear parameters, the accuracy of the reconstructions was found to be between -6mm (-2%) and 3mm, (4%). The accuracy of the current method was close to that of CT-scan reconstructions. The inter-observer variability was between 3% and 6%. Frontal and lateral X-rays are commonly obtained clinically, so 3D reconstructions can be used without increased radiation exposure to the patient.     

Large-scale 3D chromatin reconstruction from chromosomal contacts

Background

Recent advances in genome analysis have established that chromatin has preferred 3D conformations, which bring distant loci into contact. Identifying these contacts is important for us to understand possible interactions between these loci. This has motivated the creation of the Hi-C technology, which detects long-range chromosomal interactions. Distance geometry-based algorithms, such as ChromSDE and ShRec3D, have been able to utilize Hi-C data to infer 3D chromosomal structures. However, these algorithms, being matrix-based, are space- and time-consuming on very large datasets. A human genome of 100 kilobase resolution would involve ∼30,000 loci, requiring gigabytes just in storing the matrices.

Results

We propose a succinct representation of the distance matrices which tremendously reduces the space requirement. We give a complete solution, called SuperRec, for the inference of chromosomal structures from Hi-C data, through iterative solving the large-scale weighted multidimensional scaling problem.

Conclusions

SuperRec runs faster than earlier systems without compromising on result accuracy. The SuperRec package can be obtained from http://www.cs.cityu.edu.hk/~shuaicli/SuperRec.

     

3D reconstruction of dental specimens from 2D histological images and microCT-scans

Direct comparison of experimental and theoretical results in biomechanical studies requires a careful reconstruction of specimen surfaces to achieve a satisfactory congruence for validation. In this paper a semi-automatic approach is described to reconstruct triangular boundary representations from images originating from, either histological sections or microCT-, CT- or MRI-data, respectively. In a user-guided first step, planar 2D contours were extracted for every material of interest, using image segmentation techniques. In a second step, standard 2D triangulation algorithms were used to derive high quality mesh representations of the underlying surfaces. This was accomplished by converting the 2D meshes into 3D meshes by a novel lifting procedure. The meshes can be imported as is into finite element programme packages such as Marc/Mentat or COSMOS/M. Accuracy and feasibility of the algorithm is demonstrated by reconstructing several specimens as examples and comparing simulated results with available measurements performed on the original objects.     

Deep-learning-based 3D cellular force reconstruction directly from volumetric images

The forces exerted by single cells in the three-dimensional (3D) environments play a crucial role in modulating cellular functions and behaviors closely related to physiological and pathological processes. Cellular force microscopy (CFM) provides a feasible solution for quantifying mechanical interactions, which usually regains cellular forces from deformation information of extracellular matrices embedded with fluorescent beads. Owing to computational complexity, traditional 3D-CFM is usually extremely time consuming, which makes it challenging for efficient force recovery and large-scale sample analysis. With the aid of deep neural networks, this study puts forward a novel, data-driven 3D-CFM to reconstruct 3D cellular force fields directly from volumetric images with random fluorescence patterns. The deep-learning-based network is established through stacking deep convolutional neural networks (DCNN) and specific function layers. Some necessary physical information associated with constitutive relation of extracellular matrix material is coupled to the data-driven network. The mini-batch stochastic-gradient-descent and back-propagation algorithms are introduced to ensure its convergence and training efficiency. The networks not only have good generalization ability and robustness but also can recover 3D cellular forces directly from the input fluorescence image pairs. Particularly, the computational efficiency of the deep-learning-based network is at least one to two orders of magnitude higher than that of traditional 3D-CFM. This study provides a novel scheme for developing high-performance 3D-CFM to quantitatively characterize mechanical interactions between single cells and surrounding extracellular matrices, which is of vital importance for quantitative investigations in biomechanics and mechanobiology.     

3D reconstruction of mammalian septin filaments

Mammalian septins are a family of guanosine triphosphate-binding proteins thought to play a role in a number of key cellular processes, such as cytokinesis, protein scaffolding and vesicle trafficking. Although their precise functions remain to be determined, electron microscopy has shown septin filament formation in vitro and a role as a cytoskeletal polymer has been proposed. Here, we present a 3D reconstruction of septin filaments determined using electron microscopy of negatively stained specimens and single-particle image processing. Septin was isolated from rat brain as an approximately 240-kDa complex, from which immunoblotting and N-terminal sequencing identified the major components as septins 3, 5 and 7. Electron microscopy and single-particle analysis indicated that the majority of the septin filaments were ∼ 27 nm long. A comparison of 3D volumes obtained using two independent starting models (a row of spheres or a helix) and projection matching techniques revealed no major differences at the final resolution of 27 Å, and this structure was highly reproducible when the entire procedure was repeated several times. The reconstruction revealed three apparent subunits, each separated by a cleft; these subunits were similar, but not identical, possibly indicating multiple isoforms within each filament. In some views a smaller cleft appeared to separate the subunits into two smaller regions, perhaps reflecting the presence of septin dimers. This is the first 3D reconstruction of the native septin assembly, and appears compatible with the hypothesis that the septin complex is a hexamer consisting of dimers or heterotrimers. Further investigations are necessary to confirm how the structure of the filaments determined in the present study correlates with the roles of septins in vivo.     

Optimized 3D coordinate reconstruction from paired stereographs using a calibrated phantom

A refinement to a previously described three-dimensional reconstruction algorithm based on point identification in calibrated non-orthogonal radiograms (stereo-pairs) is described. The modification involves a computation of the focal point magnitude of the point in three dimensions, analogous to focusing in two dimensions, as well as the most likely location of the target point in 3-space; the focal point magnitude may be thought of as the precision of the point identification. Multiple observer studies of the same stereopair can be used to estimate three-dimensional reconstruction accuracy by providing an average location and a mean distance from average. Both measures are useful parameters for initial selection of bone landmark references and for error propagation studies.     

Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data

Chromosomes are not positioned randomly within a nucleus, but instead, they adopt preferred spatial conformations to facilitate necessary long-range gene–gene interactions and regulations. Thus, obtaining the 3D shape of chromosomes of a genome is critical for understanding how the genome folds, functions and how its genes interact and are regulated. Here, we describe a method to reconstruct preferred 3D structures of individual chromosomes of the human genome from chromosomal contact data generated by the Hi-C chromosome conformation capturing technique. A novel parameterized objective function was designed for modeling chromosome structures, which was optimized by a gradient descent method to generate chromosomal structural models that could satisfy as many intra-chromosomal contacts as possible. We applied the objective function and the corresponding optimization method to two Hi-C chromosomal data sets of both a healthy and a cancerous human B-cell to construct 3D models of individual chromosomes at resolutions of 1 MB and 200 KB, respectively. The parameters used with the method were calibrated according to an independent fluorescence in situ hybridization experimental data. The structural models generated by our method could satisfy a high percentage of contacts (pairs of loci in interaction) and non-contacts (pairs of loci not in interaction) and were compatible with the known two-compartment organization of human chromatin structures. Furthermore, structural models generated at different resolutions and from randomly permuted data sets were consistent.     

3D geometric reconstruction of thoracic aortic aneurysms

Background

Ruptured abdominal aortic aneurysms (AAAs) are the 13^th leading cause of death in the United States. While AAA rupture may occur without significant warning, its risk assessment is generally based on critical values of the maximum AAA diameter (>5 cm) and AAA-growth rate (>0.5 cm/year). These criteria may be insufficient for reliable AAA-rupture risk assessment especially when predicting possible rupture of smaller AAAs.

Methods

Based on clinical evidence, eight biomechanical factors with associated weighting coefficients were determined and summed up in terms of a dimensionless, time-dependent severity parameter, SP(t). The most important factor is the maximum wall stress for which a semi-empirical correlation has been developed.

Results

The patient-specific SP(t) indicates the risk level of AAA rupture and provides a threshold value when surgical intervention becomes necessary. The severity parameter was validated with four clinical cases and its application is demonstrated for two AAA cases.

Conclusion

As part of computational AAA-risk assessment and medical management, a patient-specific severity parameter 0 < SP(t) < 1.0 has been developed. The time-dependent, normalized SP(t) depends on eight biomechanical factors, to be obtained via a patient's pressure and AAA-geometry measurements. The resulting program is an easy-to-use tool which allows medical practitioners to make scientific diagnoses, which may save lives and should lead to an improved quality of life.     

3D geometric reconstruction of thoracic aortic aneurysms

Background  

The thoracic aortic aneurysm (TAA) is a pathology that involves an expansion of the aortic diameter in the thoracic aorta, leading to risk of rupture. Recent studies have suggested that internal wall stress, which is affected by TAA geometry and the presence or absence of thrombus, is a more reliable predictor of rupture than the maximum diameter, the current clinical criterion. Accurate reconstruction of TAA geometry is a crucial step in patient-specific stress calculations.     

Improved biocytin labeling and neuronal 3D reconstruction

In this report, we describe a reliable protocol for biocytin labeling of neuronal tissue and diaminobenzidine (DAB)-based processing of brain slices. We describe how to embed tissues in different media and how to subsequently histochemically label the tissues for light or electron microscopic examination. We provide a detailed dehydration and embedding protocol using Eukitt that avoids the common problem of tissue distortion and therefore prevents fading of cytoarchitectural features (in particular, lamination) of brain tissue; as a result, additional labeling methods (such as cytochrome oxidase staining) become unnecessary. In addition, we provide correction factors for tissue shrinkage in all spatial dimensions so that a realistic neuronal morphology can be obtained from slice preparations. Such corrections were hitherto difficult to calculate because embedding in viscous media resulted in highly nonlinear tissue deformation. Fixation, immunocytochemistry and embedding procedures for light microscopy (LM) can be completed within 42-48 h. Subsequent reconstructions and morphological analyses take an additional 24 h or more.     

3D confocal reconstruction of gene expression in mouse

Three-dimensional computer reconstructions of gene expression data will become a valuable tool in biomedical research in the near future. However, at present the process of converting in situ expression data into 3D models is a highly specialized and time-consuming procedure. Here we present a method which allows rapid reconstruction of whole-mount in situ data from mouse embryos. Mid-gestation embryos were stained with the alkaline phosphotase substrate Fast Red, which can be detected using confocal laser scanning microscopy (CLSM), and cut into 70 microm sections. Each section was then scanned and digitally reconstructed. Using this method it took two days to section, digitize and reconstruct the full expression pattern of Shh in an E9.5 embryo (a 3D model of this embryo can be seen at genex.hgu.mrc.ac.uk). Additionally we demonstrate that this technique allows gene expression to be studied at the single cell level in intact tissue.     

Ultramicroscopy: 3D reconstruction of large microscopical specimens

Ultramicroscopy is a microscopical technique that allows optical sectioning and 3D reconstruction of biological and medical specimens. While in confocal microscopy specimen size is limited to several hundred micrometers at best, using ultramicroscopy even centimeter sized objects like whole mouse embryos can be reconstructed with micrometer resolution. This is possible by using a combination of a clearing procedure and the principle of lightsheet illumination. We present ultramicroscopic 3D reconstructions of whole immunohistochemically labelled mouse embryos and adult Drosophila, giving detailed insight into their anatomy. Its speed and simplicity makes ultramicroscopy ideally suited for high‐throughput phenotype screening of transgenic mice and thus will benefit the investigation of disease models. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Assessment of race from the pelvis

Racial assessment of human postcranial skeletal remains has been a major concern for forensic and skeletal anthropologists. Materials (N = 400) of the present study are from the Terry Collection and consist of 100 black and white American pelves of both sex with known age and race. Measurements were taken from the articulated pelves. Results of discriminant function analysis indicate classificatory accuracy may be as high as 88%. Transverse pelvic breadth contributes more to the function than biiliac breadth and antero-posterior height. The females are more easily assessed racially than males. Although a highly reliable classification is produced, the results of the study should be employed with caution, as samples were of questionable nutritional status and of low socioeconomic class.     

三维技术在古昆虫复原图制作中的应用

本文简单介绍了Autodesk Maya等软件以及利用三维技术制作古昆虫复原图所涉及到的三大方面知识,包括:三维昆虫制作、场景设计和艺术气氛。较为详细的介绍了利用三维软件制作昆虫的主要步骤。总结了在制作复原图时,将生物学、计算机技术、美术学三方面知识相结合的经验和技巧。为三维技术在古昆虫学研究工作中的推广和使用提供了更多思路。     

Single particle 3D reconstruction for 2D crystal images of membrane proteins

In cases where ultra-flat cryo-preparations of well-ordered two-dimensional (2D) crystals are available, electron crystallography is a powerful method for the determination of the high-resolution structures of membrane and soluble proteins. However, crystal unbending and Fourier-filtering methods in electron crystallography three-dimensional (3D) image processing are generally limited in their performance for 2D crystals that are badly ordered or non-flat. Here we present a single particle image processing approach, which is implemented as an extension of the 2D crystallographic pipeline realized in the 2dx software package, for the determination of high-resolution 3D structures of membrane proteins. The algorithm presented, addresses the low single-to-noise ratio (SNR) of 2D crystal images by exploiting neighborhood correlation between adjacent proteins in the 2D crystal. Compared with conventional single particle processing for randomly oriented particles, the computational costs are greatly reduced due to the crystal-induced limited search space, which allows a much finer search space compared to classical single particle processing. To reduce the considerable computational costs, our software features a hybrid parallelization scheme for multi-CPU clusters and computer with high-end graphic processing units (GPUs). We successfully apply the new refinement method to the structure of the potassium channel MloK1. The calculated 3D reconstruction shows more structural details and contains less noise than the map obtained by conventional Fourier-filtering based processing of the same 2D crystal images.     

3D TOF-PET image reconstruction using total variation regularization

In this paper we introduce a semi-analytic algorithm for 3-dimensional image reconstruction for positron emission tomography (PET). The method consists of the back-projection of the acquired data into the most likely image voxel according to time-of-flight (TOF) information, followed by the filtering step in the image space using an iterative optimization algorithm with a total variation (TV) regularization. TV regularization in image space is more computationally efficient than usual iterative optimization methods for PET reconstruction with full system matrix that use TV regularization. The efficiency comes from the one-time TOF back-projection step that might also be described as a reformatting of the acquired data. An important aspect of our work concerns the evaluation of the filter operator of the linear transform mapping an original radioactive tracer distribution into the TOF back-projected image. We obtain concise, closed-form analytical formula for the filter operator. The proposed method is validated with the Monte Carlo simulations of the NEMA IEC phantom using a one-layer, 50 cm-long cylindrical device called Jagiellonian PET scanner. The results show a better image quality compared with the reference TOF maximum likelihood expectation maximization algorithm.     

Optimal calibration marker mesh for 2D X-ray sensors in 3D reconstruction

Image intensifiers suffer from distortions due to magnetic fields. In order to use this X-ray projections images for computer-assisted medical interventions, image intensifiers need to be calibrated. Opaque markers are often used for the correction of the image distortion and the estimation of the acquisition geometry parameters. Information under the markers is then lost. In this work, we consider the calibration of image intensifiers in the framework of 3D reconstruction from several 2D X-ray projections. In this context, new schemes of marker distributions are proposed for 2D X-ray sensor calibration. They are based on efficient sampling conditions of the parallel-beam X-ray transform when the detector and source trajectory is restricted to a circle around the measured object. Efficient sampling are essentially subset of standard sampling in this situation. The idea is simply to exploit the data redundancy of standard sampling and to replace some holes of efficient schemes by markers. Optimal location of markers in the sparse efficient sampling geometry can thus be found. In this case, the markers can stay on the sensor during the measurement with--theoretically--no loss of information (when the signal-to-noise ratio is large). Even if the theory is based on the parallel-beam X-ray transform, numerical experiments on both simulated and real data are shown in the case of weakly divergent beam geometry. We show that the 3D reconstruction from simulated data with interlaced markers is essentially the same as those obtained from data with no marker. We show that efficient Fourier interpolation formulas based on optimal sparse sampling schemes can be used to recover the information hidden by the markers.     

东亚飞蝗脑的形态学观察及三维重建

本文主要研究东亚飞蝗Locusta migratoria manilansis(Meyen)脑部的形态结构及其三维重建模型。采用石蜡包埋切片,在光镜下观察了东亚飞蝗脑部的形态结构,其由前脑、中脑和后脑3部分组成。为了获得整只蝗虫的连续、完整的图像数据集,采用冰冻切片技术将冰冻包埋剂(OCT)包埋的飞蝗成虫做连续切片。然后利用图像处理方法对飞蝗脑部的连续切片进行配准、分割,再用三维重建软件Image-Pro Plus(IPP)对分割后的脑部二维图像序列进行三维重建,构建出的飞蝗脑部三维结构模型可以任意旋转,能从不同角度观察。其结果为蝗虫生理和防蝗治蝗提供科学依据。