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3D reconstruction

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https://www.readbyqxmd.com/read/29344781/automated-3d-soma-segmentation-with-morphological-surface-evolution-for-neuron-reconstruction
#1
Donghao Zhang, Siqi Liu, Yang Song, Dagan Feng, Hanchuan Peng, Weidong Cai
The automatic neuron reconstruction is important since it accelerates the collection of 3D neuron models for the neuronal morphological studies. The majority of the previous neuron reconstruction methods only focused on tracing neuron fibres without considering the somatic surface. Thus, topological errors often present around the soma area in the results obtained by these tracing methods. Segmentation of the soma structures can be embedded in the existing neuron tracing methods to reduce such topological errors...
January 18, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29344776/dawning-of-a-new-era-in-trp-channel-structural-biology-by-cryo-electron-microscopy
#2
REVIEW
M Gregor Madej, Christine M Ziegler
Cryo-electron microscopy (cryo-EM) permits the determination of atomic protein structures by averaging large numbers of individual projection images recorded at cryogenic temperatures-a method termed single-particle analysis. The cryo-preservation traps proteins within a thin glass-like ice layer, making literally a freeze image of proteins in solution. Projections of randomly adopted orientations are merged to reconstruct a 3D density map. While atomic resolution for highly symmetric viruses was achieved already in 2009, the development of new sensitive and fast electron detectors has enabled cryo-EM for smaller and asymmetrical proteins including fragile membrane proteins...
January 17, 2018: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/29343858/developmental-pathways-inferred-from-modularity-morphological-integration-and-fluctuating-asymmetry-patterns-in-the-human-face
#3
Mirsha Quinto-Sánchez, Francesc Muñoz-Muñoz, Jorge Gomez-Valdes, Celia Cintas, Pablo Navarro, Caio Cesar Silva de Cerqueira, Carolina Paschetta, Soledad de Azevedo, Virginia Ramallo, Victor Acuña-Alonzo, Kaustubh Adhikari, Macarena Fuentes-Guajardo, Tábita Hünemeier, Paola Everardo, Francisco de Avila, Claudia Jaramillo, Williams Arias, Carla Gallo, Giovani Poletti, Gabriel Bedoya, Maria Cátira Bortolini, Samuel Canizales-Quinteros, Francisco Rothhammer, Javier Rosique, Andres Ruiz-Linares, Rolando Gonzalez-Jose
Facial asymmetries are usually measured and interpreted as proxies to developmental noise. However, analyses focused on its developmental and genetic architecture are scarce. To advance on this topic, studies based on a comprehensive and simultaneous analysis of modularity, morphological integration and facial asymmetries including both phenotypic and genomic information are needed. Here we explore several modularity hypotheses on a sample of Latin American mestizos, in order to test if modularity and integration patterns differ across several genomic ancestry backgrounds...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29342968/a-fast-and-robust-extrinsic-calibration-for-rgb-d-camera-networks
#4
Po-Chang Su, Ju Shen, Wanxin Xu, Sen-Ching S Cheung, Ying Luo
From object tracking to 3D reconstruction, RGB-Depth (RGB-D) camera networks play an increasingly important role in many vision and graphics applications. Practical applications often use sparsely-placed cameras to maximize visibility, while using as few cameras as possible to minimize cost. In general, it is challenging to calibrate sparse camera networks due to the lack of shared scene features across different camera views. In this paper, we propose a novel algorithm that can accurately and rapidly calibrate the geometric relationships across an arbitrary number of RGB-D cameras on a network...
January 15, 2018: Sensors
https://www.readbyqxmd.com/read/29342908/rapid-3d-reconstruction-for-image-sequence-acquired-from-uav-camera
#5
Yufu Qu, Jianyu Huang, Xuan Zhang
In order to reconstruct three-dimensional (3D) structures from an image sequence captured by unmanned aerial vehicles' camera (UAVs) and improve the processing speed, we propose a rapid 3D reconstruction method that is based on an image queue, considering the continuity and relevance of UAV camera images. The proposed approach first compresses the feature points of each image into three principal component points by using the principal component analysis method. In order to select the key images suitable for 3D reconstruction, the principal component points are used to estimate the interrelationships between images...
January 14, 2018: Sensors
https://www.readbyqxmd.com/read/29342254/distinctive-desmoplastic-3d-morphology-associated-with-brafv600e-in-papillary-thyroid-cancers
#6
M Tarabichi, A Antoniou, S Le Pennec, D Gacquer, N de Saint Aubain, L Craciun, T Cielen, I Laios, D Larsimont, G Andry, J E Dumont, C Maenhaut, V Detours
Context: Although 60% of papillary thyroid carcinomas are BRAFV600E mutant (PTCV600E), the higher aggressiveness of these cancers is still debated. Objective: In PTCV600E we aimed to further characterize the extent of the stroma and its activation, the 3D tumor-stroma interface, and the proliferation rates of tumor and stromal fibroblasts. Design: We analyzed exomes, trancriptomes and images of 364 PTC from The Cancer Genome Atlas (TCGA), including 211 PTCV600E; stained 22 independent PTC for BRAFV600E and Ki67; sequenced the exomes and stained BRAFV600E in 5 primary tumor blocks and 4 nodal metastases from one PTCV600E patient; and reconstructed the 3D volumes of one tumor and one metastatic blocks at histological resolution...
January 12, 2018: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29342123/image-based-localization-aided-indoor-pedestrian-trajectory-estimation-using-smartphones
#7
Yan Zhou, Xianwei Zheng, Ruizhi Chen, Hanjiang Xiong, Sheng Guo
Accurately determining pedestrian location in indoor environments using consumer smartphones is a significant step in the development of ubiquitous localization services. Many different map-matching methods have been combined with pedestrian dead reckoning (PDR) to achieve low-cost and bias-free pedestrian tracking. However, this works only in areas with dense map constraints and the error accumulates in open areas. In order to achieve reliable localization without map constraints, an improved image-based localization aided pedestrian trajectory estimation method is proposed in this paper...
January 17, 2018: Sensors
https://www.readbyqxmd.com/read/29341715/potential-energy-surface-reconstruction-and-lifetime-determination-of-molecular-double-core-hole-states-in-the-hard-x-ray-regime
#8
T Marchenko, G Goldsztejn, K Jänkälä, O Travnikova, L Journel, R Guillemin, N Sisourat, D Céolin, M Žitnik, M Kavčič, K Bučar, A Mihelič, B Cunha de Miranda, I Ismail, A F Lago, F Gel'mukhanov, R Püttner, M N Piancastelli, M Simon
A combination of resonant inelastic x-ray scattering and resonant Auger spectroscopy provides complementary information on the dynamic response of resonantly excited molecules. This is exemplified for CH_{3}I, for which we reconstruct the potential energy surface of the dissociative I 3d^{-2} double-core-hole state and determine its lifetime. The proposed method holds a strong potential for monitoring the hard x-ray induced electron and nuclear dynamic response of core-excited molecules containing heavy elements, where ab initio calculations of potential energy surfaces and lifetimes remain challenging...
September 29, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29341616/stochasticity-of-pores-interconnectivity-in-li-o2-batteries-and-its-impact-on-the-variations-in-electrochemical-performance
#9
Amangeldi Torayev, José Alexis Rucci, Pieter M Magusin, Arnaud Demortiere, Vincent De Andrade, Clare P Grey, Céline Merlet, Alejandro A Franco
While large dispersions in electrochemical performance have been reported for lithium oxygen batteries in the literature, they have not been investigated in any depth. The variability in the results is often assumed to arise from differences in cell design, electrode structure, handling and cell preparation at different times. An accurate theoretical framework turns out to be needed to get a better insight into the mechanisms underneath and to interpreting experimental results. Here, we develop and use a pore network model to simulate the electrochemical performance of three-dimensionally resolved lithium-oxygen cathode mesostructures obtained from TXM nano-computed tomography images...
January 17, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29340238/a-revised-cranial-description-of-massospondylus-carinatus-owen-dinosauria-sauropodomorpha-based-on-computed-tomographic-scans-and-a-review-of-cranial-characters-for-basal-sauropodomorpha
#10
Kimberley E J Chapelle, Jonah N Choiniere
Massospondylus carinatus is a basal sauropodomorph dinosaur from the early Jurassic Elliot Formation of South Africa. It is one of the best-represented fossil dinosaur taxa, known from hundreds of specimens including at least 13 complete or nearly complete skulls. Surprisingly, the internal cranial anatomy of M. carinatus has never been described using computed tomography (CT) methods. Using CT scans and 3D digital representations, we digitally reconstruct the bones of the facial skeleton, braincase, and palate of a complete, undistorted cranium of M...
2018: PeerJ
https://www.readbyqxmd.com/read/29339792/assemble-and-match-a-novel-hybrid-tool-for-enhancing-education-and-research-in-rational-structure-based-drug-design
#11
Pouya Tavousi, Reza Amin, Sina Shahbazmohamadi
Rational drug design is the process of finding new medication that can activate or inhibit the biofunction of a target molecule by binding to it and forming a molecular complex. Here, shape and charge complementarities between drug and target are key. To help find effective drug molecules out of a huge pool of possibilities, physical and computer aided tools have been developed. Former offers a tangible experience of the molecular interactions yet lacks measurement and evaluation capabilities. Latter enables accurate and fast evaluations, but does not deliver the interactive tangible experience of physical models...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29339575/dynamic-pet-image-reconstruction-integrating-temporal-regularization-associated-with-respiratory-motion-correction-for-applications-in-oncology
#12
Thibaut Merlin, Dimitris Visvikis, Philippe Fernandez, Frederic Lamare
Respiratory motion reduces both the qualitative and quantitative accuracy of PET images in oncology. This impact is more significant for quantitative applications based on kinetic modeling, where dynamic acquisitions are associated with limited statistics due to the necessity of enhanced temporal resolution. The aim of this study is to address these drawbacks by combining within a unique reconstruction algorithm in dynamic PET imaging, a respiratory motion correction approach, as well as a temporal regularization...
January 17, 2018: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/29338903/clinical-workflow-optimization-to-improve-4dct-reconstruction-for-toshiba-aquilion-ct-scanners
#13
P Freislederer, C Heinz, H von Zimmermann, S Gerum, F Roeder, M Reiner, M Söhn, C Belka, K Parodi
Respiratory motion remains a source of major uncertainties in radiotherapy. Respiratory correlated computed tomography (referred to as 4DCT) serves as one way of reducing breathing artifacts in 3D-CTs and allows the investigation of tumor motion over time. The quality of the 4DCT images depends on the data acquisition scheme, which in turn is dependent on the vendor. Specifically, the only way Toshiba Aquilion LB CT scanners can reconstruct 4DCTs is a cycle-based reconstruction using triggers provided by an external surrogate signal...
January 12, 2018: Zeitschrift Für Medizinische Physik
https://www.readbyqxmd.com/read/29337113/volta-phase-plate-data-collection-facilitates-image-processing-and-cryo-em-structure-determination
#14
Ottilie von Loeffelholz, Gabor Papai, Radostin Danev, Alexander G Myasnikov, S Kundhavai Natchiar, Isabelle Hazemann, Jean-François Ménétret, Bruno P Klaholz
A current bottleneck in structure determination of macromolecular complexes by cryo electron microscopy (cryo-EM) is the large amount of data needed to obtain high-resolution 3D reconstructions, including through sorting into different conformations and compositions with advanced image processing. Additionally, it may be difficult to visualize small ligands that bind in sub-stoichiometric levels. Volta phase plates (VPP) introduce a phase shift in the contrast transfer and drastically increase the contrast of the recorded low-dose cryo-EM images while preserving high frequency information...
January 11, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29336922/segmentation-free-direct-tumor-volume-and-metabolic-activity-estimation-from-pet-scans
#15
Saeid Asgari Taghanaki, Noirin Duggan, Hillgan Ma, Xinchi Hou, Anna Celler, Francois Benard, Ghassan Hamarneh
Tumor volume and metabolic activity are two robust imaging biomarkers for predicting early therapy response in F-fluorodeoxyglucose (FDG) positron emission tomography (PET), which is a modality to image the distribution of radiotracers and thereby observe functional processes in the body. To date, estimation of these two biomarkers requires a lesion segmentation step. While the segmentation methods requiring extensive user interaction have obvious limitations in terms of time and reproducibility, automatically estimating activity from segmentation, which involves integrating intensity values over the volume is also suboptimal, since PET is an inherently noisy modality...
December 27, 2017: Computerized Medical Imaging and Graphics: the Official Journal of the Computerized Medical Imaging Society
https://www.readbyqxmd.com/read/29336877/sin-quadratic-model-for-chest-tomosynthesis-respiratory-signal-analysis-and-its-application-in-four-dimensional-chest-tomosynthesis-reconstruction
#16
Xi Tao, Hua Zhang, Genggeng Qin, Jianhua Ma, Qianjin Feng, Wufan Chen
Chest tomosynthesis (CTS) is a newly developed imaging technique which provides pseudo-3D volume anatomical information of thorax from limited-angle projections and contains much less of superimposed anatomy than the chest X-ray radiography. One of the relatively common problems in CTS is the patient respiratory motion during image acquisition, which negatively impacts the detectability. In this work, we propose a sin-quadratic model to analyze the respiratory motion during CTS scan, which is a real time method where the respiratory signal is generated by extracting the motion of diaphragm from projection radiographs...
January 11, 2018: Medical Engineering & Physics
https://www.readbyqxmd.com/read/29336490/progress-towards-a-methodology-for-high-throughput-3d-reconstruction-of-soot-nanoparticles-via-electron-tomography
#17
E Haffner-Staton, A LA Rocca, M W Fay
The aim of this work is to make progress towards the development of 3D reconstruction as a legitimate alternative to traditional 2D characterization of soot. Time constraints are the greatest opposition to its implementation, as currently reconstruction of a single soot particle takes around 5-6 h to complete. As such, the accuracy and detail gains are currently insufficient to challenge 2D characterization of a representative sample (e.g. 200 particles). This work is a consideration of the optimization of the steps included within the computational reconstruction and manual segmentation of soot particles...
January 16, 2018: Journal of Microscopy
https://www.readbyqxmd.com/read/29335485/electron-beam-melting-in-the-fabrication-of-three-dimensional-mesh-titanium-mandibular-prosthesis-scaffold
#18
Rongzeng Yan, Danmei Luo, Haitao Huang, Runxin Li, Niu Yu, Changkui Liu, Min Hu, Qiguo Rong
The study was designed to fulfill effective work-flow to fabricate three-dimensional mesh titanium scaffold for mandibular reconstruction. The 3D titanium mesh scaffold was designed based on a volunteer with whole mandible defect. (1) acquisition of the CT data; (2) design with computer aided design (CAD) and finite element analysis (FEA). The pore size and intervals with the best mechanic strength was also calculated using FEA. (3) fabrication of the scaffold using electron beam melting (EBM); (4) implantation surgery...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29334989/implantation-of-a-3d-printed-titanium-sternum-in-a-patient-with-a-sternal-tumor
#19
Anton Dzian, Jozef Živčák, Rastislav Penciak, Radovan Hudák
BACKGROUND: Primary malignant or metastatic sternal tumors are uncommon. A subtotal or total sternectomy can offer a radical form of treatment. The issue is to restore the structural integrity of the chest wall. CASE PRESENTATION: We report the implantation of an individualized 3D-printed titanium sternum in a patient with a sternal tumor. CONCLUSIONS: We believe that tridimensional print technologies may also change the strategy of chest wall reconstruction...
January 15, 2018: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/29334799/potential-of-epr-spin-trapping-to-investigate-in-situ-free-radicals-generation-from-skin-allergens-in-reconstructed-human-epidermis-cumene-hydroperoxide-as-proof-of-concept
#20
Salen Kuresepi, Bertrand Vileno, Philippe Turek, Jean-Pierre Lepoittevin, Elena Giménez-Arnau
The first step in the development of skin sensitisation to a chemical, and in the elicitation of further allergic contact dermatitis (ACD), is the binding of the allergen to skin proteins after penetrating into the epidermis. The so-formed antigenic adduct is then recognised by the immune system as foreign to the body. Sensitising organic hydroperoxides derived from autoxidation of natural terpenes are believed to form antigens through radical-mediated mechanisms, although this has not yet been established...
January 15, 2018: Free Radical Research
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