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High-density 3D mapping

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
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
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
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
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
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
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
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
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
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
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
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
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
Nicole Schubert, Markus Axer, Martin Schober, Anh-Minh Huynh, Marcel Huysegoms, Nicola Palomero-Gallagher, Jan G Bjaalie, Trygve B Leergaard, Mehmet E Kirlangic, Katrin Amunts, Karl Zilles
High-resolution multiscale and multimodal 3D models of the brain are essential tools to understand its complex structural and functional organization. Neuroimaging techniques addressing different aspects of brain organization should be integrated in a reference space to enable topographically correct alignment and subsequent analysis of the various datasets and their modalities. The Waxholm Space ( is a publicly available 3D coordinate-based standard reference space for the mapping and registration of neuroanatomical data in rodent brains...
2016: Frontiers in Neuroanatomy
Richard L Blackmon, Rupninder Sandhu, Brian S Chapman, Patricia Casbas-Hernandez, Joseph B Tracy, Melissa A Troester, Amy L Oldenburg
The mammary gland extracellular matrix (ECM) is comprised of biopolymers, primarily collagen I, that are created and maintained by stromal fibroblasts. ECM remodeling by fibroblasts results in changes in ECM fiber spacing (pores) that have been shown to play a critical role in the aggressiveness of breast cancer. However, minimally invasive methods to measure the spatial distribution of ECM pore areas within tissues and in vitro 3D culture models are currently lacking. We introduce diffusion-sensitive optical coherence tomography (DS-OCT) to image the nanoscale porosity of ECM by sensing weakly constrained diffusion of gold nanorods (GNRs)...
April 26, 2016: Biophysical Journal
Amber Miller, Lukkana Suksanpaisan, Shruthi Naik, Rebecca Nace, Mark Federspiel, Kah Whye Peng, Stephen J Russell
Systemically administered oncolytic viruses have the ability to cause tumor destruction through the expansion and coalescence of intratumoral infectious centers. Efficacy is therefore dependent upon both the density and intratumoral distribution of virus-infected cells achieved after initial virus infusion, and delivery methods are being developed to enhance these critical parameters. However, the three-dimensional (3D) mapping of intratumoral infectious centers is difficult using conventional immunohistochemical methodology, requiring painstaking 3D reconstruction of numerous sequential stained tumor sections, with no ability to study the temporal evolution of spreading infection in a single animal...
2014: Molecular Therapy Oncolytics
Evan Levine, Bruce Daniel, Shreyas Vasanawala, Brian Hargreaves, Manojkumar Saranathan
PURPOSE: To enable robust, high spatio-temporal-resolution three-dimensional Cartesian MRI using a scheme incorporating a novel variable density random k-space sampling trajectory allowing flexible and retrospective selection of the temporal footprint with compressed sensing (CS). METHODS: A complementary Poisson-disc k-space sampling trajectory was designed to allow view sharing and varying combinations of reduced view sharing with CS from the same prospective acquisition...
April 21, 2016: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
Sohail Zahid, Hubert Cochet, Patrick M Boyle, Erica L Schwarz, Kaitlyn N Whyte, Edward J Vigmond, Rémi Dubois, Mélèze Hocini, Michel Haïssaguerre, Pierre Jaïs, Natalia A Trayanova
AIMS: The mechanisms underlying persistent atrial fibrillation (AF) in patients with atrial fibrosis are poorly understood. The goal of this study was to use patient-derived atrial models to test the hypothesis that AF re-entrant drivers (RDs) persist only in regions with specific fibrosis patterns. METHODS AND RESULTS: Twenty patients with persistent AF (PsAF) underwent late gadolinium-enhanced MRI to detect the presence of atrial fibrosis. Segmented images were used to construct personalized 3D models of the fibrotic atria with biophysically realistic atrial electrophysiology...
June 1, 2016: Cardiovascular Research
Mengmeng Yang, Yuanjun Yang, Bin Hong, Liangxin Wang, Kai Hu, Yongqi Dong, Han Xu, Haoliang Huang, Jiangtao Zhao, Haiping Chen, Li Song, Huanxin Ju, Junfa Zhu, Jun Bao, Xiaoguang Li, Yueliang Gu, Tieying Yang, Xingyu Gao, Zhenlin Luo, Chen Gao
Mechanism of metal-insulator transition (MIT) in strained VO2 thin films is very complicated and incompletely understood despite three scenarios with potential explanations including electronic correlation (Mott mechanism), structural transformation (Peierls theory) and collaborative Mott-Peierls transition. Herein, we have decoupled coactions of structural and electronic phase transitions across the MIT by implementing epitaxial strain on 13-nm-thick (001)-VO2 films in comparison to thicker films. The structural evolution during MIT characterized by temperature-dependent synchrotron radiation high-resolution X-ray diffraction reciprocal space mapping and Raman spectroscopy suggested that the structural phase transition in the temperature range of vicinity of the MIT is suppressed by epitaxial strain...
2016: Scientific Reports
Jose Javier Conesa, Joaquín Otón, Michele Chiappi, Jose María Carazo, Eva Pereiro, Francisco Javier Chichón, José L Carrascosa
We used soft X-ray three-dimensional imaging to quantify the mass of superparamagnetic iron oxide nanoparticles (SPION) within whole cells, by exploiting the iron oxide differential absorption contrast. Near-edge absorption soft X-ray nanotomography (NEASXT) combines whole-cell 3D structure determination at 50 nm resolution, with 3D elemental mapping and high throughput. We detected three-dimensional distribution of SPIONs within cells with 0.3 g/cm(3) sensitivity, sufficient for detecting the density corresponding to a single nanoparticle...
2016: Scientific Reports
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