3D Evaluation of the acetabular coverage assessed by biplanar X-rays or single anteroposterior X-ray compared with CT-scan

Considering the increasing development of three dimensional (3D) imaging, the 3D assessment of the acetabular coverage is to become the most interesting tool for the detection of acetabular pathologies. Biplanar X-rays based methods allow a 3D reconstruction of the hip with a reduced radiation dose. This study proposes a 3D assessment method of the acetabular coverage from biplanar X-rays or from an anteroposterior X-ray (conventional clinical imaging). An in vitro evaluation of the method was performed on six hip joints in comparison with computed tomography. The global coverage, the local coverage and the acetabular rim orientation were estimated in 3D. The mean global acetabular coverage was 40% with an estimated mean accuracy of 1.3% for the biplanar X-rays based method. This study evaluated a 3D assessment method of the acetabular coverage from biplanar X-rays or anteroposterior X-ray and open the way for clinical in vivo applications.     

3D Evaluation of the acetabular coverage assessed by biplanar X-rays or single anteroposterior X-ray compared with CT-scan

Considering the increasing development of three dimensional (3D) imaging, the 3D assessment of the acetabular coverage is to become the most interesting tool for the detection of acetabular pathologies. Biplanar X-rays based methods allow a 3D reconstruction of the hip with a reduced radiation dose. This study proposes a 3D assessment method of the acetabular coverage from biplanar X-rays or from an anteroposterior X-ray (conventional clinical imaging). An in vitro evaluation of the method was performed on six hip joints in comparison with computed tomography. The global coverage, the local coverage and the acetabular rim orientation were estimated in 3D. The mean global acetabular coverage was 40% with an estimated mean accuracy of 1.3% for the biplanar X-rays based method. This study evaluated a 3D assessment method of the acetabular coverage from biplanar X-rays or anteroposterior X-ray and open the way for clinical in vivo applications.     

Fast 3D reconstruction of the lower limb using a parametric model and statistical inferences and clinical measurements calculation from biplanar X-rays

In clinical routine, lower limb analysis relies on conventional X-ray (2D view) or computerised tomography (CT) Scan (lying position). However, these methods do not allow 3D analysis in standing position. The aim of this study is to propose a fast and accurate 3D-reconstruction-method based on parametric models and statistical inferences from biplanar X-rays with clinical measurements' (CM) assessment in standing position for a clinical routine use. For the reproducibility study, the 95% CI was under 2.7° for all lower limbs' angular measurements except for tibial torsion, femoral torsion and tibiofemoral rotation (?相似文献   

Fast 3D reconstruction of the lower limb using a parametric model and statistical inferences and clinical measurements calculation from biplanar X-rays

In clinical routine, lower limb analysis relies on conventional X-ray (2D view) or computerised tomography (CT) Scan (lying position). However, these methods do not allow 3D analysis in standing position. The aim of this study is to propose a fast and accurate 3D-reconstruction-method based on parametric models and statistical inferences from biplanar X-rays with clinical measurements' (CM) assessment in standing position for a clinical routine use. For the reproducibility study, the 95% CI was under 2.7° for all lower limbs' angular measurements except for tibial torsion, femoral torsion and tibiofemoral rotation ( < 5°). The 95% CI were under 2.5 mm for lower limbs' lengths and 1.5 to 3° for the pelvis' CM. Comparisons between X-rays and CT-scan based 3D shapes in vitro showed mean differences of 1.0 mm (95% CI = 2.4 mm). Comparisons of 2D lower limbs' and 3D pelvis' CM between standing ‘Shifted-Feet’ and ‘Non-Shifted-Feet’ position showed means differences of 0.0 to 1.4°. Significant differences were found only for pelvic obliquity and rotation. The reconstruction time was about 5 min.     

3D reconstruction of the pelvis from bi-planar radiography

3D personalized models are more and more requested for clinical and biomechanical studies. Techniques based on bi-planar X-rays present the advantage of a low radiation dose for the patient. However, up to now, such techniques have shown limited accuracy in the case of pelvis reconstruction. This study proposes and validates a method providing accurate 3D personalized model of the pelvis from bi-planar X-rays. The algorithm is based on the fast computation of an initial solution followed by local deformations based on 2D anatomical points and contours that are digitized in both radiographs. Results were close to CT-scan reconstructions (mean difference 1.6 mm and differences under 4.3 mm for 95% of the points). Moreover, 3D morphometry of the pelvis could be obtained with an accuracy of 5%. This technique provides 3D patient specific model with a low radiation dose.     

Geometry of human ribs pertinent to orthopedic chest-wall reconstruction

Orthopedic reconstruction of blunt chest trauma can aid restoration of pulmonary function to reduce the mortality associated with serial rib fractures and flail chest injuries. Contemporary chest wall reconstruction requires contouring of generic plates to the complex surface geometry of ribs. This study established a biometric foundation to generate specialized, anatomically contoured osteosynthesis hardware for rib fracture fixation. On human cadaveric ribs three through nine, the surface geometry pertinent to anatomically conforming osteosynthesis plates was characterized by quantifying the apparent rib curvature C(A), the longitudinal twist alpha(LT) along the diaphysis, and the unrolled curvature C(U). In addition, the rib cross-sectional geometry pertinent to intramedullary fixation strategies was characterized in terms of cross-section height, width, area, and cortex thickness. The rib surface exhibited a curvature C(A) ranging from 3.8 m(-1) in the anteromedial section of rib seven to 17.3 m(-1) in the posterior section of rib three. All ribs had in common a longitudinal twist alpha(LT), ranging from 41-60 degrees. The unrolled curvature C(U) decreased gradually from ribs three to five, and increased gradually with reversed orientation from rib six to nine. The cross-sectional area remained constant along the rib diaphysis. However, the medullary canal increased in size from 29.9 mm(2) posteriorly to 41.2 mm(2) in anterior rib segments. Results of this biometric rib characterization describe a novel strategy for intraoperative plate contouring and provide a foundation for the development of specialized rib osteosynthesis strategies.     

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 and comparison of shapes of DNA minicircles observed by cryo-electron microscopy

We use cryo-electron microscopy to compare 3D shapes of 158 bp long DNA minicircles that differ only in the sequence within an 18 bp block containing either a TATA box or a catabolite activator protein binding site. We present a sorting algorithm that correlates the reconstructed shapes and groups them into distinct categories. We conclude that the presence of the TATA box sequence, which is believed to be easily bent, does not significantly affect the observed shapes.     

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.     

In-air versus underwater comparison of 3D reconstruction accuracy using action sport cameras

Action sport cameras (ASC) have achieved a large consensus for recreational purposes due to ongoing cost decrease, image resolution and frame rate increase, along with plug-and-play usability. Consequently, they have been recently considered for sport gesture studies and quantitative athletic performance evaluation. In this paper, we evaluated the potential of two ASCs (GoPro Hero3+) for in-air (laboratory) and underwater (swimming pool) three-dimensional (3D) motion analysis as a function of different camera setups involving the acquisition frequency, image resolution and field of view. This is motivated by the fact that in swimming, movement cycles are characterized by underwater and in-air phases what imposes the technical challenge of having a split volume configuration: an underwater measurement volume observed by underwater cameras and an in-air measurement volume observed by in-air cameras. The reconstruction of whole swimming cycles requires thus merging of simultaneous measurements acquired in both volumes. Characterizing and optimizing the instrumental errors of such a configuration makes mandatory the assessment of the instrumental errors of both volumes.In order to calibrate the camera stereo pair, black spherical markers placed on two calibration tools, used both in-air and underwater, and a two-step nonlinear optimization were exploited. The 3D reconstruction accuracy of testing markers and the repeatability of the estimated camera parameters accounted for system performance. For both environments, statistical tests were focused on the comparison of the different camera configurations. Then, each camera configuration was compared across the two environments. In all assessed resolutions, and in both environments, the reconstruction error (true distance between the two testing markers) was less than 3mm and the error related to the working volume diagonal was in the range of 1:2000 (3×1.3×1.5 m³) to 1:7000 (4.5×2.2×1.5 m³) in agreement with the literature. Statistically, the 3D accuracy obtained in the in-air environment was poorer (p<10⁻⁵) than the one in the underwater environment, across all the tested camera configurations. Related to the repeatability of the camera parameters, we found a very low variability in both environments (1.7% and 2.9%, in-air and underwater). This result encourage the use of ASC technology to perform quantitative reconstruction both in-air and underwater environments.     

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。     

3D Sequential Kinematics of the Femoro-Tibial Joint of Normal Knee from Multiple Bi-planar X-rays: Accuracy and Repeatability

Background

Several methods can be used to assess joint kinematics going from optoelectronic motion analysis to biplanar fluoroscopy. The aim of the present work was to evaluate the reliability of the use of biplane radiography to quantify the sequential 3D kinematics of the femoro-tibial joint.

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 and manufacture of real abdominal aortic aneurysms: from CT scan to silicone model

Abdominal aortic aneurysm (AAA) can be defined as a permanent and irreversible dilation of the infrarenal aorta. AAAs are often considered to be an aorta with a diameter 1.5 times the normal infrarenal aorta diameter. This paper describes a technique to manufacture realistic silicone AAA models for use with experimental studies. This paper is concerned with the reconstruction and manufacturing process of patient-specific AAAs. 3D reconstruction from computed tomography scan data allows the AAA to be created. Mould sets are then designed for these AAA models utilizing computer aided designcomputer aided manufacture techniques and combined with the injection-moulding method. Silicone rubber forms the basis of the resulting AAA model. Assessment of wall thickness and overall percentage difference from the final silicone model to that of the computer-generated model was performed. In these realistic AAA models, wall thickness was found to vary by an average of 9.21%. The percentage difference in wall thickness recorded can be attributed to the contraction of the casting wax and the expansion of the silicone during model manufacture. This method may be used in conjunction with wall stress studies using the photoelastic method or in fluid dynamic studies using a laser-Doppler anemometry. In conclusion, these patient-specific rubber AAA models can be used in experimental investigations, but should be assessed for wall thickness variability once manufactured.     

Perforator flaps from the lateral lower leg for intraoral reconstruction

Perforator flaps are based on cutaneous, small-diameter vessels that originate from a main pedicle and perforate fascia or muscle to reach the skin. Although these flaps have recently become popular for soft-tissue reconstructions in nearly all regions of the body, the systematic application of perforator flaps with short, small-caliber pedicles for intraoral reconstruction has not been reported. Experience with the use of 10 consecutive perforator flaps from the lateral lower leg for intraoral defect coverage is reported. In 10 cases, a 4- to 6-cm-long septocutaneous or myocutaneous perforating vessel from the peroneal artery, with a diameter of 1 to 2 mm, could be identified in the proximal one-half of the lateral lower leg. The thin, pliable skin paddles, measuring up to 6 x 8 cm, were used for defect coverage after resection of squamous cell carcinomas of the floor of the mouth (five cases), soft palate (one case), tongue (two cases), or buccal mucosa (two cases). Anastomoses were performed to the lingual artery and concomitant vein. Except for one case, all perforator flaps healed without complications and the functional results were satisfying. At the donor site, which was always closed directly, an approximately 15-cm-long scar resulted, without functional impairments. The peroneal artery was regularly preserved. Perforator flaps from the lateral lower leg might have many applications for intraoral soft-tissue reconstruction, especially because of their minimal donor-site morbidity.     

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.     

Synthesis and biological activity of 3 beta-fluorovitamin D3: comparison of the biological activity of 3 beta-fluorovitamin D3 and 3-deoxyvitamin D3

The alteration in the biologic activity of the vitamin D3 molecule resulting from the replacement of a hydrogen atom with a fluorine atom is a subject of fundamental interest. To investigate this problem we synthesized 3 beta-fluorovitamin D3 6 and its hydrogen analog, 3-deoxyvitamin D3 7, and tested the biologic activity of each by in vitro and in vivo methods. Contrary to previous reports which showed that 3 beta-fluorovitamin D3 was as active as vitamin D3 in vivo, we found that the fluoro-analog was less active than vitamin D3. With regard to stimulation of intestinal calcium transport and bone calcium mobilization in the D-deficient hypocalcemic rat, 3 beta-fluorovitamin D3 showed significantly greater biologic activity than its hydrogen analog, 3-deoxyvitamin D3. In the organ-cultured, embryonic chick duodenum, 3 beta-fluorovitamin D3 was approx 1/1000th as active as the native hormone, 1,25-dihydroxyvitamin D3, while 3-deoxyvitamin D3 was inactive even at microM concentrations, in the induction of the vitamin D-dependent, calcium-binding protein. With regard to in vitro activity in displacing radiolabeled 25-hydroxyvitamin D3 from vitamin D binding protein and radiolabelled 1,25-dihydroxyvitamin D3 from a chick intestinal cytosol receptor, 3 beta-fluorovitamin D3 and 3 beta-deoxyvitamin D3 both showed very poor binding efficiencies when compared with vitamin D3. Our results show that the substitution of a fluorine atom for a hydrogen atom at the C-3 position of the vitamin D3 molecule results in a fluorovitamin 6 with significantly more biological activity than its hydrogen analog, 3-deoxyvitamin D3 7.     

Cortactin binding to F-actin revealed by electron microscopy and 3D reconstruction

Cortactin and WASP activate Arp2/3-mediated actin filament nucleation and branching. However, different mechanisms underlie activation by the two proteins, which rely on distinct actin-binding modules and modes of binding to actin filaments. It is generally thought that cortactin binds to "mother" actin filaments, while WASP donates actin monomers to Arp2/3-generated "daughter" filament branches. Interestingly, cortactin also binds WASP in addition to F-actin and the Arp2/3 complex. However, the structural basis for the role of cortactin in filament branching remains unknown, making interpretation difficult. Here, electron microscopy and 3D reconstruction were carried out on F-actin decorated with the actin-binding repeating domain of cortactin, revealing conspicuous density on F-actin attributable to cortactin that is located on a consensus-binding site on subdomain-1 of actin subunits. Strikingly, the binding of cortactin widens the gap between the two long-pitch filament strands. Although other proteins have been found to alter the structure of the filament, the cortactin-induced conformational change appears unique. The results are consistent with a mechanism whereby alterations of the F-actin structure may facilitate recruitment of the Arp2/3 complex to the "mother" filament in the cortex of cells. In addition, cortactin may act as a structural adapter protein, stabilizing nascent filament branches while mediating the simultaneous recruitment of Arp2/3 and WASP.     

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.