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3D visualization

Sabrina Dorn, Shuqing Chen, Stefan Sawall, Joscha Maier, Michael Knaup, Monika Uhrig, Heinz-Peter Schlemmer, Andreas Maier, Michael Lell, Marc Kachelrieß
PURPOSE: To establish a novel paradigm to facilitate radiologists' workow: combining mutually exclusive CT image properties that emerge from different reconstructions, display settings and organ-dependent spectral evaluation methods into a single context-sensitive imaging by exploiting prior anatomical information. METHODS: The CT dataset is segmented and classified into different organs, e.g. the liver, left and right kidney, spleen, aorta and left and right lung, as well as into the tissue types bone, fat, soft tissue and vessels using a cascaded 3D fully convolutional neural network (CNN) consisting of two successive 3D U-nets...
August 11, 2018: Medical Physics
Nora N Sommer, Karla M Treitl, Eva Coppenrath, Hendrik Kooijman, Claudia Dechant, Michael Czihal, Theresa M Kolben, Sebastian E Beyer, Wieland H Sommer, Tobias Saam
OBJECTIVES: Arteritic anterior ischemic optic neuropathy (A-AION) caused by inflammatory occlusion of the posterior ciliary arteries is the most common reason for irreversible vision loss in patients with giant cell arteritis. Atypical clinical presentation and negative funduscopy can delay systemic high-dose corticosteroid therapy to prevent impending permanent blindness and involvement of the contralateral eye.The purpose of this study was to assess the diagnostic accuracy of 3-dimensional (3D) high-resolution T1-weighted black-blood magnetic resonance imaging (T1-BB-MRI) for the detection of posterior ciliary artery involvement in patients with giant cell arteritis and funduscopic A-AION...
August 8, 2018: Investigative Radiology
Erol Özgür, Bongjin Koo, Bertrand Le Roy, Emmanuel Buc, Adrien Bartoli
PURPOSE: Augmented reality for monocular laparoscopy from a preoperative volume such as CT is achieved in two steps. The first step is to segment the organ in the preoperative volume and reconstruct its 3D model. The second step is to register the preoperative 3D model to an initial intraoperative laparoscopy image. To date, there does not exist an automatic initial registration method to solve the second step for the liver in the de facto operating room conditions of monocular laparoscopy...
August 9, 2018: International Journal of Computer Assisted Radiology and Surgery
Karina van den Broek, Mirco Daniel, Matthias Epple, Hubert Kuhn, Jonas Schaub, Achim Zielesny
Simplified Particle Input ConnEction Specification (SPICES) is a particle-based molecular structure representation derived from straightforward simplifications of the atom-based SMILES line notation. It aims at supporting tedious and error-prone molecular structure definitions for particle-based mesoscopic simulation techniques like Dissipative Particle Dynamics by allowing for an interplay of different molecular encoding levels that range from topological line notations and corresponding particle-graph visualizations to 3D structures with support of their spatial mapping into a simulation box...
August 9, 2018: Journal of Cheminformatics
Lubin Gou, Wei Zhang, Chuanming Li, Xinlin Shi, Zhiming Zhou, Weijia Zhong, Ting Chen, Xiajia Wu, Chun Yang, Dajing Guo
Purpose: Depression is common in Parkinson's disease (PD) and is correlated with the severity of motor deficits and quality of life. The present study aimed to investigate alterations in the structural brain network related to depression in Parkinson's disease (d-PD) and their correlations with structural impairments of white matter (WM). Materials and Methods: Data were acquired from the Parkinson Progression Markers Initiative (PPMI) database. A total of 84 de novo and drug-naïve PD patients were screened and classified into two groups according to the 15-item Geriatric Depression Scale (GDS-15): d-PD ( n = 28) and nondepression in PD (nd-PD, n = 56)...
2018: Frontiers in Neurology
Paul L Rosin, Yu-Kun Lai, Chang Liu, Graham R Davis, David Mills, Gary Tuson, Yuki Russell
There is a large body of historical documents that are too fragile to be opened or unrolled, making their contents inaccessible. Recent improvements in X-ray scanning technology and computer vision techniques make it possible to perform a "virtual" unrolling of such documents. We describe a novel technique to process a stack of 3D X-ray images to identify the surface of parchment scrolls, unroll them, and create a visualization of their written contents. Unlike existing techniques, we can handle even challenging cases with minimal manual interaction...
August 9, 2018: Scientific Reports
Camille Clément, Guillermo A Orsi, Alberto Gatto, Ekaterina Boyarchuk, Audrey Forest, Bassam Hajj, Judith Miné-Hattab, Mickaël Garnier, Zachary A Gurard-Levin, Jean-Pierre Quivy, Geneviève Almouzni
DNA replication is a challenge for the faithful transmission of parental information to daughter cells, as both DNA and chromatin organization must be duplicated. Replication stress further complicates the safeguard of epigenome integrity. Here, we investigate the transmission of the histone variants H3.3 and H3.1 during replication. We follow their distribution relative to replication timing, first in the genome and, second, in 3D using super-resolution microscopy. We find that H3.3 and H3.1 mark early- and late-replicating chromatin, respectively...
August 9, 2018: Nature Communications
Michael El Boghdady, Gobinath Ramakrishnan, Afshin Alijani
AIM: There are reports of visual strains and associated symptoms when operating in a 3D laparoscopic environment. We aimed to study the extent of visual symptoms seen in 3D versus conventional 2D imaging in volunteers performing laparoscopic tasks and study the effect of eye exercises on 3D laparoscopy. METHODS: Twenty four consented laparoscopic novices were required to undergo a visual acuity test (Snellen chart) and eye deviation test (Maddox Wing). A battery of specific isolated laparoscopic tasks lasting 30 min was developed to test their ability to detect changes in 2D and 3D environments separately...
August 3, 2018: American Journal of Surgery
Thierry Pécot, Liu Zengzhen, Jérôme Boulanger, Jean Salamero, Charles Kervrann
Analysis of the spatial distribution of endomembrane trafficking is fundamental to understand the mechanisms controlling cellular dynamics, cell homeostasy, and cell interaction with its external environment in normal and pathological situations. We present a semi-parametric framework to quantitatively analyze and visualize the spatio-temporal distribution of intracellular events from different conditions. From the spatial coordinates of intracellular features such as segmented subcellular structures or vesicle trajectories, QuantEv automatically estimates weighted densities that are easy to interpret and performs a comprehensive statistical analysis from distribution distances...
August 9, 2018: ELife
Katie Grogan, Laura Ferguson
On Tuesday evenings at New York University School of Medicine (NYUSoM), the anatomy lab is transformed into an art studio. Medical students gather with a spirit of creative enterprise and a unique goal: to turn anatomy into art. They are participants in Art & Anatomy, an innovative drawing course within the Master Scholars Program in Humanistic Medicine (MSPHM)-a component of NYUSoM, which offers elective courses across a range of interdisciplinary topics in medical humanities. Art & Anatomy has had approximately four hundred fifty participants since its inception in 2009...
August 8, 2018: Journal of Medical Humanities
Vebjørn Ekroll, Kathleen Mertens, Johan Wagemans
We report results from an experiment showing that a tall pillar with a triangular base evokes radically different three-dimensional (3D) percepts depending on the vantage point from which it is observed. The base of the pillar is an isosceles right triangle, but the pillar is perceived as just a thin plane when viewed from some vantage points. Viewed from other vantage points, the perceived 3D shape of the pillar corresponds to a square or rectangular base. In general, our results suggest that the visual system uses a preference for rectangularity (or symmetry) to determine the 3D shape of objects...
May 2018: I-Perception
Francis Abed Rabbo, Guillaume Koch, Christian Lefèvre, Romuald Seizeur
PURPOSE: To study the white matter tracts connecting the different stereoscopic visual areas of the brain by diffusion tensor imaging. METHODS: In a previous study, we identified the cortical activations to a visual 3D stimulation in 12 subjects using functional MRI (fMRI). These areas of cortical activations [V5, V6, lateral occipital complex (LOC) and intra parietal sulcus areas (IPS)] in addition to the lateral geniculate nucleus (LGN) and the primary visual area V1 were chosen as regions of interest (ROIs)...
August 7, 2018: Surgical and Radiologic Anatomy: SRA
Axel Newe, Linda Becker
BACKGROUND: The Portable Document Format (PDF) is the standard file format for the communication of biomedical information via the internet and for electronic scholarly publishing. Although PDF allows for the embedding of three-dimensional (3D) objects and although this technology has great potential for the communication of such data, it is not broadly used by the scientific community or by clinicians. OBJECTIVE: The objective of this review was to provide an overview of existing publications that apply 3D PDF technology and the protocols and tools for the creation of model files and 3D PDFs for scholarly purposes to demonstrate the possibilities and the ways to use this technology...
August 7, 2018: JMIR Medical Informatics
Sheng Wang, Shiyang Fei, Zongan Wang, Yu Li, Jinbo Xu, Feng Zhao, Xin Gao
Summary: PredMP is the first web service, to our knowledge, that aims at de novo prediction of the membrane protein (MP) 3D structure followed by the embedding of the MP into the lipid bilayer for visualization. Our approach is based on a high-throughput Deep Transfer Learning (DTL) method that first predicts MP contacts by learning from non-MPs and then predicts the 3D model of the MP using the predicted contacts as distance restraints. This algorithm is derived from our previous Deep Learning (DL) method originally developed for soluble protein contact prediction, which has been officially ranked No...
August 4, 2018: Bioinformatics
Josef Neumüller
Electron tomography (ET) was developed to overcome some of the problems associated reconstructing three-dimensional (3D) images from 2D election microscopy data from ultrathin slices. Virtual sections of semithin sample are obtained by incremental rotation of the target and this information is used to assemble a 3D image. Herein, we provide an instruction to ET including the physical principle, possibilities, and limitations. We review the development of innovative methods and highlight important investigations performed in our department and with our collaborators...
August 6, 2018: Wiener Medizinische Wochenschrift
Mauricio Carrillo-Tripp, Leonardo Alvarez-Rivera, Omar Israel Lara-Ramírez, Francisco Javier Becerra-Toledo, Adan Vega-Ramírez, Emmanuel Quijas-Valades, Eduardo González-Zavala, Julio Cesar González-Vázquez, Javier García-Vieyra, Nelly Beatriz Santoyo-Rivera, Sergio Victor Chapa-Vergara, Amilcar Meneses-Viveros
Research on biology has seen significant advances with the use of molecular dynamics (MD) simulations. The MD methodology enables explanation and discovery of molecular mechanisms in a wide range of natural processes and biological systems. The need to readily share the ever-increasing amount of MD data has been hindered by the lack of specialized bioinformatic tools. The difficulty lies in the efficient management of the data, i.e., in sending and processing 3D information for its visualization. In this work, we present HTMoL, a plug-in-free, secure GPU-accelerated web application specifically designed to stream and visualize MD trajectory data on a web browser...
August 6, 2018: Journal of Computer-aided Molecular Design
Vered H Eisenberg, Geertje Callewaert, Nikhil Sindhwani, Susanne Housmans, Dominique van Schoubroeck, Lior Lowenstein, Jan Deprest
INTRODUCTION AND HYPOTHESIS: Paramagnetic Fe particles can be added during synthetic mesh production to allow visibility on magnetic resonance imaging. Our aim was to evaluate whether transperineal ultrasound (TPUS) allows visualization, measurement, and characterization of polyvinylidene fluoride (PVDF mesh) containing Fe particles compared with regular polypropylene (PP) meshes used for sacrocolpopexy. METHODS: Women up to 1.5 years after laparoscopic sacrocolpopexy who were implanted with a PP or PVDF mesh underwent clinical examination and 2D, 3D, and 4D TPUS...
August 6, 2018: International Urogynecology Journal
Pietro Amodeo, Enrico D'Aniello, Fanny Defranoux, Angela Marino, Livia D'Angelo, Michael T Ghiselin, Ernesto Mollo
Fish have proven to be valuable models in the study of the endocrine control of appetite in response to peripheral signals of energetic and nutritional status. In parallel, a growing body of literature points to the importance of sensory experiences as factors affecting food choice in fish, with a special focus on visual and chemical signals allowing discrimination of potential foods within a 3D environment. Accordingly, waterborne compounds, such as monosaccharides or amino acids, are regarded as the main "olfactory" cues driving fish alimentary behavior...
2018: Results and Problems in Cell Differentiation
Yan Han, Chunli Yan, Susan Fishbain, Ivaylo Ivanov, Yuan He
RNA polymerase III (Pol III) transcription initiation requires the action of the transcription factor IIIB (TFIIIB) and is highly regulated. Here, we determine the structures of Pol III pre-initiation complexes (PICs) using single particle cryo-electron microscopy (cryo-EM). We observe stable Pol III-TFIIIB complexes using nucleic acid scaffolds mimicking various functional states, in which TFIIIB tightly encircles the upstream promoter DNA. There is an intricate interaction between TFIIIB and Pol III, which stabilizes the winged-helix domains of the C34 subunit of Pol III over the active site cleft...
2018: Cell Discovery
Chi-Lun Lin, Dane Coffey, Daniel Keefe, Arthur Erdman
Design by Dragging (DBD) [1] is a virtual design tool, which displays three-dimensional (3D) visualizations of many simulation results obtained by sampling a large design space and ties this visual display together with a new user interface. The design space is explored through mouse-based interactions performed directly on top of the 3D data visualizations. Our previous study [1] introduced the realization of DBD with a simplistic example of biopsy needle design under a static bending force. This paper considers a realistic problem of designing a vacuum-assisted biopsy (VAB) needle that brings in more technical challenges to include dynamic tissue reaction forces, nonlinear tissue deformation, and progressive tissue damage in an integrated visualization with design suggestions...
June 2018: Journal of Medical Devices
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