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High-density 3D mapping

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https://www.readbyqxmd.com/read/28048563/we-ab-207b-05-correlation-of-normal-lung-density-changes-with-dose-after-stereotactic-body-radiotherapy-sbrt-for-early-stage-lung-cancer
#1
Q Wu, S Devpura, K Feghali, C Liu, M Ajlouni, B Movsas, I Chetty
PURPOSE: To investigate correlation of normal lung CT density changes with dose accuracy and outcome after SBRT for patients with early stage lung cancer. METHODS: Dose distributions for patients originally planned and treated using a 1-D pencil beam-based (PB-1D) dose algorithm were retrospectively recomputed using algorithms: 3-D pencil beam (PB-3D), and model-based METHODS: AAA, Acuros XB (AXB), and Monte Carlo (MC). Prescription dose was 12 Gy × 4 fractions...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048395/we-fg-206-07-assessing-the-lung-function-of-patients-with-non-small-cell-lung-cancer-using-hyperpolarized-xenon-129-dissolved-phase-mri
#2
K Qing, J Mugler, Q Chen
PURPOSE: Hyperpolarized xenon-129 dissolved-phase MRI is the first imaging technique that allows 3-dimensional regional mapping of ventilation and gas uptake by tissue and blood the in human lung. Multiple outcome measures can be produced from this method. Existing studies in subjects with major lung diseases compared to healthy controls demonstrated high sensitivities of this method to pulmonary physiological factors including ventilation, alveolar tissue density, surface-to-volume ratio, pulmonary perfusion and gas-blood barrier thickness...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048262/su-g-iep1-07-inaccuracy-of-lesion-blood-flow-quantification-related-to-the-proton-density-reference-image-in-arterial-spin-labeling-mri-of-brain-tumors
#3
M Jen, J Johnson, P Hou, H Liu
PURPOSE: Cerebral blood flow quantification in arterial spin labeling (ASL) MRI requires an estimate of the equilibrium magnetization of blood, which is often obtained by a set of proton density (PD) reference image. Normally, a constant blood-brain partition coefficient is assumed across the brain. However, this assumption may not be valid for brain lesions. This study aimed to evaluate the impact of lesion-related PD variations on ASL quantification in patients with brain tumors. METHODS: MR images for posttreatment evaluation of 42 patients with brain tumors were retrospectively analyzed...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047789/su-g-iep2-13-toward-heavy-ion-computed-tomography-with-carbon-ions-a-monte-carlo-study
#4
D Shrestha, N Qin, Y Zhang, X Jia, J Wang
PURPOSE: In the present Monte Carlo study, we investigated the use of Carbon ions for computed tomography (CT) with a relatively low imaging dose. This will enable us to avoid any conversion of X-ray CT numbers to the relative stopping power (or relative electron density) values and the associated uncertainties in Carbon dose calculation. METHODS: In the first stage, we studied the propagation of Carbon nuclei through a water phantom using the Geant4 specially to understand their lateral displacement inside the phantom...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046474/th-ab-209-04-3d-light-sheet-luminescence-imaging-with-cherenkov-radiation
#5
P Bruza, H Lin, L Jarvis, D Gladstone, B Pogue
PURPOSE: To recover a three-dimensional density distribution of luminescent molecular probes located several centimeters deep within a highly scattering tissue. METHODS: We developed a novel sheet beam Cherenkov-excited luminescence scanned imaging (CELSI) methodology. The sample was irradiated by a horizontally oriented, vertically scanned 6 MV X-ray sheet beam (200mm × 5mm, 0.2mm vertical step) from a radiotherapy linear accelerator. The resulting Cherenkov light emission - and thus luminescent probe excitation - occurred exclusively along the irradiation plane due to a short diffusion path of secondary particles and Cherenkov photons...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28018953/high-resolution-three-dimensional-quantitative-map-of-the-macromolecular-proton-fraction-distribution-in-the-normal-rat-brain
#6
Anna V Naumova, Andrey E Akulov, Marina Yu Khodanovich, Vasily L Yarnykh
The presented dataset provides a normative high-resolution three-dimensional (3D) macromolecular proton fraction (MPF) map of the healthy rat brain in vivo and source images used for its reconstruction. The images were acquired using the protocol described elsewhere (Naumova, et al. High-resolution three-dimensional macromolecular proton fraction mapping for quantitative neuroanatomical imaging of the rodent brain in ultra-high magnetic fields. Neuroimage (2016) doi: 10.1016/j.neuroimage.2016.09.036). The map was reconstructed from three source images with different contrast weightings (proton density, T1, and magnetization transfer) using the single-point algorithm with a synthetic reference image...
February 2017: Data in Brief
https://www.readbyqxmd.com/read/28011432/challenges-in-quantitative-crystallographic-characterization-of-3d-thin-films-by-acom-tem
#7
A Kobler, C Kübel
Automated crystal orientation mapping for transmission electron microscopy (ACOM-TEM) has become an easy to use method for the investigation of crystalline materials and complements other TEM methods by adding local crystallographic information over large areas. It fills the gap between high resolution electron microscopy and electron back scatter diffraction in terms of spatial resolution. Recent investigations showed that spot diffraction ACOM-TEM is a quantitative method with respect to sample parameters like grain size, twin density, orientation density and others...
July 5, 2016: Ultramicroscopy
https://www.readbyqxmd.com/read/27881953/connectomic-analysis-of-brain-networks-novel-techniques-and-future-directions
#8
REVIEW
J Leonie Cazemier, Francisco Clascá, Paul H E Tiesinga
Brain networks, localized or brain-wide, exist only at the cellular level, i.e., between specific pre- and post-synaptic neurons, which are connected through functionally diverse synapses located at specific points of their cell membranes. "Connectomics" is the emerging subfield of neuroanatomy explicitly aimed at elucidating the wiring of brain networks with cellular resolution and a quantified accuracy. Such data are indispensable for realistic modeling of brain circuitry and function. A connectomic analysis, therefore, needs to identify and measure the soma, dendrites, axonal path, and branching patterns together with the synapses and gap junctions of the neurons involved in any given brain circuit or network...
2016: Frontiers in Neuroanatomy
https://www.readbyqxmd.com/read/27854315/3d-scene-reconstruction-using-omnidirectional-vision-and-lidar-a-hybrid-approach
#9
Michiel Vlaminck, Hiep Luong, Werner Goeman, Wilfried Philips
In this paper, we propose a novel approach to obtain accurate 3D reconstructions of large-scale environments by means of a mobile acquisition platform. The system incorporates a Velodyne LiDAR scanner, as well as a Point Grey Ladybug panoramic camera system. It was designed with genericity in mind, and hence, it does not make any assumption about the scene or about the sensor set-up. The main novelty of this work is that the proposed LiDAR mapping approach deals explicitly with the inhomogeneous density of point clouds produced by LiDAR scanners...
November 16, 2016: Sensors
https://www.readbyqxmd.com/read/27831864/3d-myocardial-elastography-in-vivo
#10
Clement Papadacci, Ethan A Bunting, Elaine Y Wan, Pierre Nauleau, Elisa E Konofagou
Strain evaluation is of major interest in clinical cardiology as it can quantify the cardiac function. Myocardial elastography, a radio-frequency (RF)-based cross-correlation method, has been developed to evaluate the local strain distribution in the heart in vivo. However, inhomogeneities such as RF ablation lesions or infarction require a three-dimensional approach to be measured accurately. In addition, acquisitions at high volume rate are essential to evaluate the cardiac strain in three dimensions. Conventional focused transmit schemes using 2D matrix arrays, trade off sufficient volume rate for beam density or sector size to image rapid moving structure such as the heart, which lowers accuracy and precision in the strain estimation...
November 1, 2016: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/27813164/3d-accelerated-stack-of-spirals-acquisitions-and-reconstruction-of-arterial-spin-labeling-mri
#11
Yulin V Chang, Marta Vidorreta, Ze Wang, John A Detre
PURPOSE: The goal of this study was to develop a 3D acceleration and reconstruction method to improve image quality and resolution of background-suppressed arterial spin-labeled perfusion MRI. METHODS: Accelerated acquisition was implemented in all three k-space dimensions in a stack-of-spirals readout using variable density spirals and partition undersampling. A single 3D self-consistent parallel imaging (SPIRiT) kernel was calibrated and iteratively applied to reconstruct each imaging volume...
November 3, 2016: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/27796326/shedding-light-on-cell-compartmentation-in-the-candidate-phylum-poribacteria-by-high-resolution-visualisation-and-transcriptional-profiling
#12
Martin T Jahn, Sebastian M Markert, Taewoo Ryu, Timothy Ravasi, Christian Stigloher, Ute Hentschel, Lucas Moitinho-Silva
Assigning functions to uncultivated environmental microorganisms continues to be a challenging endeavour. Here, we present a new microscopy protocol for fluorescence in situ hybridisation-correlative light and electron microscopy (FISH-CLEM) that enabled, to our knowledge for the first time, the identification of single cells within their complex microenvironment at electron microscopy resolution. Members of the candidate phylum Poribacteria, common and uncultivated symbionts of marine sponges, were used towards this goal...
October 31, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27770164/diffusion-weighted-endorectal-mr-imaging-at-3t-for-prostate-cancer-correlation-with-tumor-cell-density-and-percentage-gleason-pattern-on-whole-mount-pathology
#13
Daniel I Glazer, Elmira Hassanzadeh, Andriy Fedorov, Olutayo I Olubiyi, Shayna S Goldberger, Tobias Penzkofer, Trevor A Flood, Paul Masry, Robert V Mulkern, Michelle S Hirsch, Clare M Tempany, Fiona M Fennessy
OBJECTIVE: To determine if tumor cell density and percentage of Gleason pattern within an outlined volumetric tumor region of interest (TROI) on whole-mount pathology (WMP) correlate with apparent diffusion coefficient (ADC) values on corresponding TROIs outlined on pre-operative MRI. METHODS: Men with biopsy-proven prostate adenocarcinoma undergoing multiparametric MRI (mpMRI) prior to prostatectomy were consented to this prospective study. WMP and mpMRI images were viewed using 3D Slicer and each TROI from WMP was contoured on the high b-value ADC maps (b0, 1400)...
October 22, 2016: Abdominal Radiology
https://www.readbyqxmd.com/read/27725258/foil-hole-and-data-image-quality-assessment-in-3dem-towards-high-throughput-image-acquisition-in-the-electron-microscope
#14
J Vargas, E Franken, C O S Sorzano, J Gomez-Blanco, R Schoenmakers, A J Koster, J M Carazo
Automatic or semiautomatic data collection approaches on a transmission electron microscope (TEM) for Single Particle Analysis, capable of acquiring large datasets composed of only high quality images, are of great importance to obtain 3D density maps with the highest resolution possible. Typically, this task is performed by an experienced microscopist, who manually decides to keep or discard images according to subjective criteria. Therefore, this methodology is slow, intensive in human work and subjective...
December 2016: Journal of Structural Biology
https://www.readbyqxmd.com/read/27628179/large-scale-localization-of-touching-somas-from-3d-images-using-density-peak-clustering
#15
Shenghua Cheng, Tingwei Quan, Xiaomao Liu, Shaoqun Zeng
BACKGROUND: Soma localization is an important step in computational neuroscience to map neuronal circuits. However, locating somas from large-scale and complicated datasets is challenging. The challenges primarily originate from the dense distribution of somas, the diversity of soma sizes and the inhomogeneity of image contrast. RESULTS: We proposed a novel localization method based on density-peak clustering. In this method, we introduced two quantities (the local density ρ of each voxel and its minimum distance δ from voxels of higher density) to describe the soma imaging signal, and developed an automatic algorithm to identify the soma positions from the feature space (ρ, δ)...
2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27585189/measuring-connectivity-in-the-primary-visual-pathway-in-human-albinism-using-diffusion-tensor-imaging-and-tractography
#16
Anahit Grigorian, Larissa McKetton, Keith A Schneider
In albinism, the number of ipsilaterally projecting retinal ganglion cells (RGCs) is significantly reduced. The retina and optic chiasm have been proposed as candidate sites for misrouting. Since a correlation between the number of lateral geniculate nucleus (LGN) relay neurons and LGN size has been shown, and based on previously reported reductions in LGN volumes in human albinism, we suggest that fiber projections from LGN to the primary visual cortex (V1) are also reduced. Studying structural differences in the visual system of albinism can improve the understanding of the mechanism of misrouting and subsequent clinical applications...
2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27577508/homogeneity-and-variation-of-donor-doping-in-verneuil-grown-srtio3-nb-single-crystals
#17
C Rodenbücher, M Luysberg, A Schwedt, V Havel, F Gunkel, J Mayer, R Waser
The homogeneity of Verneuil-grown SrTiO3:Nb crystals was investigated. Due to the fast crystal growth process, inhomogeneities in the donor dopant distribution and variation in the dislocation density are expected to occur. In fact, for some crystals optical studies show variations in the density of Ti(3+) states on the microscale and a cluster-like surface conductivity was reported in tip-induced resistive switching studies. However, our investigations by TEM, EDX mapping, and 3D atom probe reveal that the Nb donors are distributed in a statistically random manner, indicating that there is clearly no inhomogeneity on the macro-, micro-, and nanoscale in high quality Verneuil-grown crystals...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27572730/tools-for-model-building-and-optimization-into-near-atomic-resolution-electron-cryo-microscopy-density-maps
#18
F DiMaio, W Chiu
Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described...
2016: Methods in Enzymology
https://www.readbyqxmd.com/read/27325527/characterization-mapping-and-ablation-of-complex-atrial-tachycardia-initial-experience-with-a-novel-method-of-ultra-high-density-3d-mapping
#19
Benjamin Schaeffer, Boris A Hoffmann, Christian Meyer, Ruken Ö Akbulak, Julia Moser, Mario Jularic, Christian Eickholt, Jana M Nührich, Pawel Kuklik, Stephan Willems
INTRODUCTION: Conventional mapping of complex atrial tachycardias (AT) can be challenging. Thus, we evaluated feasibility and utility of a novel, ultra high-density 3D mapping approach to characterize and map AT in these cases. METHODS AND RESULTS: Overall, 21 patients (67.4±7.6 years; male: 52.4%, 1.9±1.4 previous ablation procedures) with documented AT referred to our center underwent catheter ablation including ultra high-density mapping using a novel 64-electrode mini-basket catheter and an adjunctive 3D mapping system...
June 21, 2016: Journal of Cardiovascular Electrophysiology
https://www.readbyqxmd.com/read/27246003/dense-small-molecule-labeling-enables-activator-dependent-storm-by-proximity-mapping
#20
Ye Chen, Min Gu, Peter W Gunning, Sarah M Russell
Stochastic optical reconstruction microscopy (STORM) enables high-resolution imaging, but multi-channel 3D imaging is problematic because of chromatic aberrations and alignment errors. The use of activator-dependent STORM in which spectrally distinct activators can be coupled with a single reporter can circumvent such issues. However, the standard approach of linking activators and reporters to a single antibody molecule is hampered by low labeling density and the large size of the antibody. We proposed that small molecule labels might enable activator-dependent STORM if the reporter or activator were linked to separate small molecules that bound within 3...
September 2016: Histochemistry and Cell Biology
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