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High-density 3D mapping

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...
October 8, 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
João L Salinet, Nicholas Masca, Peter J Stafford, G André Ng, Fernando S Schlindwein
BACKGROUND: Areas with high frequency activity within the atrium are thought to be 'drivers' of the rhythm in patients with atrial fibrillation (AF) and ablation of these areas seems to be an effective therapy in eliminating DF gradient and restoring sinus rhythm. Clinical groups have applied the traditional FFT-based approach to generate the three-dimensional dominant frequency (3D DF) maps during electrophysiology (EP) procedures but literature is restricted on using alternative spectral estimation techniques that can have a better frequency resolution that FFT-based spectral estimation...
2016: Biomedical Engineering Online
Mykhailo Monchak, Thomas Hupfer, Anatoliy Senyshyn, Hans Boysen, Dmitry Chernyshov, Thomas Hansen, Karl G Schell, Ethel C Bucharsky, Michael J Hoffmann, Helmut Ehrenberg
The Al-substituted LiTi2(PO4)3 powders Li(1+x)Al(x)Ti(2-x)(PO4)3 (LATP) were successfully prepared by a water-based sol-gel process with subsequent calcination and sintering. The crystal structure of obtained samples was characterized at different temperatures using high-resolution synchrotron-based X-ray and neutron powder diffraction. Possible lithium diffusion pathways were initially evaluated using the difference bond-valence approach. Experimental 3D lithium diffusion pathway in LATP was extracted from the negative nuclear density maps reconstructed by the maximum entropy method...
March 21, 2016: Inorganic Chemistry
Nicolas Navarro, A Murat Maga
We describe the application of high-resolution 3D microcomputed tomography, together with 3D landmarks and geometric morphometrics, to validate and further improve previous quantitative genetic studies that reported QTL responsible for variation in the mandible shape of laboratory mice using a new backcross between C57BL/6J and A/J inbred strains. Despite the increasing availability of 3D imaging techniques, artificial flattening of the mandible by 2D imaging techniques seems at first an acceptable compromise for large-scale phenotyping protocols, thanks to an abundance of low-cost digital imaging systems such as microscopes or digital cameras...
2016: G3: Genes—Genomes—Genetics
J Vargas, J Otón, R Marabini, J M Carazo, C O S Sorzano
Electron Microscopy is reaching new capabilities thanks to the combined effect of new technologies and new image processing methods. However, the reconstruction process is still complex, requiring many steps and elaborated optimization procedures. Therefore, the possibility to reach a wrong structure exists, justifying the need of robust statistical tests. In this work, we present a conceptually simple alignment test, which does not require tilt-pair images, to evaluate the alignment consistency between a set of projection images with respect to a given 3D density map...
2016: Scientific Reports
Michael M Zeineh, Nicola Palomero-Gallagher, Markus Axer, David Gräβel, Maged Goubran, Andreas Wree, Roger Woods, Katrin Amunts, Karl Zilles
While hippocampal connectivity is essential to normal memory function, our knowledge of human hippocampal circuitry is largely inferred from animal studies. Using polarized light microscopy at 1.3 µm resolution, we have directly visualized the 3D course of key medial temporal pathways in 3 ex vivo human hemispheres and 2 ex vivo vervet monkey hemispheres. The multiple components of the perforant path system were clearly identified: Superficial sheets of fibers emanating from the entorhinal cortex project to the presubiculum and parasubiculum, intermixed transverse and longitudinal angular bundle fibers perforate the subiculum and then project to the cornu ammonis (CA) fields and dentate molecular layer, and a significant alvear component runs from the angular bundle to the CA fields...
February 13, 2016: Cerebral Cortex
Fang-zuo Li, Zhi-guo Liu, Tian-xi Sun, Long-tao Yi, Wei-gang Zhao, Jia-lin He, Song Peng, Li-li Wang, Guang-cui Zhao, Xun-liang Ding
Confocal three dimensional (3D) micro X-ray fluorescence (XRF) spectrometer based on a polycapillary focusing X-ray lens (PFXRL) in the excitation channel and a polycapillary parallel X-ray lens (PPXRL) in the detection channel was developed. The PFXRL and PPXRL were placed in a confocal configuration. This was helpful in improving the signal-to-noise ratio of the XRF spectra, and accordingly lowered the detection limitation of the XRF technology. The confocal configuration ensured that only the XRF signal from the confocal micro-volume overlapped by the output focal spot of the PFXRL and the input focal spot of the PPXRL could be detected by the detector...
September 2015: Guang Pu Xue Yu Guang Pu Fen Xi, Guang Pu
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