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THE RELEVANCE OF DOSE-FRACTIONATION IN TOMOGRAPHY OF RADIATION-SENSITIVE SPECIMENS

ULTRAMICROSCOPY 1995年第3期60卷 357-373页

作者： MCEWEN, BF DOWNING, KH GLAESER, RM UNIV CALIF BERKELEY LAWRENCE BERKELEY LABSDIV LIFE SCIBERKELEYCA 94720 UNIV CALIF BERKELEY DEPT MOLEC & CELL BIOLBERKELEYCA 94720

It is commonly assumed that the number of projections required for single-axis tomography precludes its application to most beam-labile specimens. However, Hegerl and Hoppe have pointed out that the total dose required to achieve statistical significance for each voxel of a computed 3D reconstruction is the same as that required to obtain a single 2D image of that isolated voxel, at the same level of statistical significance. Thus a statistically significant 3D image can be computed from statistically insignificant projections, as long as the total dose that is distributed among these projections is high enough that it would have resulted in a statistically significant projection, if applied to only one image. We have tested this critical theorem by simulating the tomographic reconstruction of a realistic 3D model created from an electron micrograph. The simulations verify the basic conclusions of the theorem and extend its validity to the experimentally more realistic conditions of high absorption, signal-dependent noise, varying specimen contrast and missing angular range. Individual projections in the series of fractionated-dose images could be aligned by cross-correlation because they contained significant information derived from the summation of features from different depths in the structure. This latter information is generally not useful for structural interpretation prior to 3D reconstruction, owing to the complexity of most specimens investigated by single-axis tomography. These results demonstrate that it is feasible to use single-axis tomography with soft X-ray and electron microscopy of frozen-hydrated specimens.

关键词： Centrioles/ultrastructure Centrioles/ultrastructure computer Simulation image processing, computer-assisted/methods Microscopy/methods Microscopy, Electron/methods Radiation Tolerance Tomography/methods X-Rays X-Rays

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AUTOMATED MICROSCOPY FOR ELECTRON TOMOGRAPHY

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ULTRAMICROSCOPY 1992年第1-4期46卷 207-227页

作者： KOSTER, AJ CHEN, H SEDAT, JW AGARD, DA UNIV CALIF SAN FRANCISCO HOWARD HUGHES MED INSTSAN FRANCISCOCA 94143

Instrumentation and methodology for the automatic collection of tomographic tilt series data for the three-dimensional reconstruction of single particles is described. The system consists of a Philips EM 430 TEM, with a Gatan 673 cooled slow-scan CCD camera and a Philips C400 microscope computer control unit attached. The procedure for data collection includes direct digital recording of the images on the CCD camera and the automatic measurement and correction of (a) image shifts resulting from tilting the specimen, (b) variation of defocus and (c) the eucentric height position of the specimen. Experiments are described illustrating the possibilities and limitations of automatic data collection. Data collection at a magnification of 30k shows that the exposure time of the specimen to the beam is reduced by a factor of 10-100 compared to manual operation of the TEM.

关键词： Artifacts Chromatin/ultrastructure image processing, computer-assisted/instrumentation image processing, computer-assisted/methods Microscopy, Electron/instrumentation Microscopy, Electron/methods Models, Theoretical Tomography

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Multiframe particle tracking in intravital imaging: defining Lagrangian coordinates in the microcirculation

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BIOTECHNIQUES 2006年第5期41卷 597-601页

作者： Ravnic, Dino J. Tsuda, Akira Turhan, Aslihan Pratt, Juan P. Huss, Harold T. Zhang, Yu-Zhong Mentzer, Steven J. Harvard Univ Sch Med Boston MA USA Harvard Univ Sch Publ Hlth Boston MA 02115 USA Mol Probes Invitrogen Eugene OR USA

The cellular composition of the microcirculation creates blood flow that can be unsteady and nonuniform. To obtain information about nonuniform cellular trajectories, we describe in vivo imaging techniques that provide both detailed tracking of individual particles as well as an approach to simultaneous multicolor particle tracking. Particularly relevant to biologic systems, Lagrangian methods provide information about the fate of individual particles and flow in the system.

关键词： Animals image processing, computer-assisted/methods Male Mice Mice, Inbred BALB C Microcirculation/cytology Microcirculation/physiology Microscopy, Video/methods Nanoparticles

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Stereo-4-D reconstruction and animation from living fluorescent specimens

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BIOTECHNIQUES 1998年第6期24卷 1006-+页

作者： Mohler, WA White, JG Univ Wisconsin Mol Biol Lab Madison WI 53706 USA

We present a novel approach to the viewing and analysis of 4-dimensional (4-D) data sets recorded from live fluorescent samples. With stereo-4-D reconstructions, the observer manipulates a rotatable projection of the full 3-dimensional (3-D) specimen while simultaneously controlling animation of the recording forward or backward in time. The result is a unique lifelike perspective on the development of an entire living subject. Here, we apply this technique to the observation of the cell membranes of developing Caenorhabditis elegans. Embryos labeled with the vital plasma membrane probe FM(TM) 4-64 were imaged by multiphoton laser scanning fluorescence microscopy, yielding 4-D data sets of entire embryos over several hours of development. Stereo 4-D and standard focal-plane 4-D viewing of these novel time-lapse recordings provide the observer with detail at both the subcellular and whole-animal level from a single data set and produce a unique record of the lineage, cell shape changes, cell contacts and morphogenetic dynamics that make up embryogenesis. The procedures by which stereo-4-D reconstructions are created and viewed rely on public domain software running on a personal computer and should therefore be accessible by a general audience. Data output utilizes the versatile and well-supported QuickTime(TM) animation format. Additional features allow for stereo-4-D reconstruction of isolated 3-D volumes of interest from within the larger specimen.

关键词： Animals Caenorhabditis elegans/embryology Database Management Systems Databases, Factual image processing, computer-assisted/instrumentation image processing, computer-assisted/methods Microscopy, Fluorescence/methods Microscopy, Video/instrumentation Microscopy, Video/methods Software Video Recording/methods

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A Background Color Scheme for Piper Plots to Spatially Visualize Hydrochemical Patterns

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GROUNDWATER 2014年第1期52卷 2-6页

作者： Peeters, Luk CSIRO Land & Water Groundwater Hydrol Program Glen Osmond SA 5064 Australia

The combination of ternary diagrams of cations and anions with a central diamond graph make the Piper plot very useful in visualizing groundwater chemistry datasets. One of the major drawbacks is that it is hard to link spatial attributes of the dataset to the plot. In this study, we propose a background color scheme of the Piper plot so that spatial representations of these data can be colored according to their location in the Piper plot. The color scheme is chosen to have maximum resolution while still being perceptually uniform. The linking between Piper plot and maps through this color scheme allows the interpretation of the trends and processes deduced from the Piper plot in terms of the location in the aquifer, the geology, and the groundwater flow dynamics. The colored Piper plot is applied to a groundwater quality dataset of the Condamine Alluvium in Queensland, Australia.

关键词： Anions Cations Color Databases, Factual Environmental Monitoring/methods Groundwater image processing, computer-assisted/methods Maps as Topic Potassium/analysis Queensland Radium/analysis Thorium/analysis Water Quality

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Organic-inorganic hybrid liquid crystals:: Thermotropic mesophases formed by hybridization of liquid-crystalline phosphates and monodispersed α-Fe₂O₃ particles

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JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 2005年第33期127卷 11578-11579页

作者： Kanie, K Muramatsu, A Tohoku Univ Inst Multidisciplinary Res Adv Mat Aoba Ku Sendai Miyagi 9808577 Japan

Nano-level hybridization of organic and inorganic materials has attracted agreat deal of attention,especially in the fields of material science and nanotechnology,because itis not rare to find unexpected superadditive *** liquid crystals (LCs) areanisotropic materials of an enormous variety of dynamic and self-assembling functions,and thus theintroduction of such functions into organic materials has been a useful technique in *** the other hand,recent progress of particle deposition systems,such as the gel-solmethod,enabled us to obtain mono-dispersed particles precisely controlled in size and *** the gel-sol method,we have reported a facile procedure for the preparation of monodispersedalpha-Fe_2O_3 particles with various shapes and sizes by the addition of shape controllers and *** example,in the presence of PO_4~(3-) ions,monodispersed spindle-type alpha-Fe_2O_3particles have been readily obtained.

关键词： Crystallization Ferrous Compounds/chemical synthesis Ferrous Compounds/chemical synthesis Ferrous Compounds/chemistry Ferrous Compounds/chemistry image processing, computer-assisted/methods Microscopy, Electron, Transmission/methods Nanostructures/chemistry Organometallic Compounds/chemical synthesis Organometallic Compounds/chemistry Particle Size Phosphates/chemical synthesis Phosphates/chemical synthesis Phosphates/chemistry Phosphates/chemistry Temperature

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A NEW AUTOMATED-METHOD OF image-ANALYSIS - COMPARISON OF CILIARY AND FLAGELLAR BEATS

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BIORHEOLOGY 1990年第3-4期27卷 567-579页

作者： SCHOEVAERT, D MARANO, F SERRES, C BERREBAH, H UNIV PARIS 07 CYTOPHYSIOL & TOXICOL CELLULAIRE LABCNRSUA 567F-75251 PARIS 05FRANCE

A new automated method of image analysis of sperm flagellar (human) and cilia (Dunaliella) bends is developed. This method permits an automatic determination of the line characterizing the flagellum. Two dynamic parameters are measured: the wave propagation velocity and the wave curvature radius. The data reveal similar patterns in the propagation of the principal and reverse waves between flagelated and ciliated cells. Conversely, differences are seen in principal wave curvature due perhaps to the presence of periaxonemal structures in the flagellum, absent in cilium. The identical patterns of reverse wave curvaturei in both systems may be linked to axonemal limitations.

关键词： Algae/physiology Cilia/physiology Flagella/physiology Humans image processing, computer-assisted/methods Male Motion Pictures as Topic Movement/physiology Sperm Tail/physiology

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Tomographic 3D reconstruction of quick-frozen, Ca²⁺-activated contracting insect flight muscle

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CELL 1999年第4期99卷 421-431页

作者： Taylor, KA Schmitz, H Reedy, MC Goldman, YE Franzini-Armstrong, C Sasaki, H Tregear, RT Poole, K Lucaveche, C Edwards, RJ Chen, LF Winkler, H Reedy, MK Florida State Univ Inst Mol Biophys Tallahassee FL 32306 USA Univ Penn Penn Muscle Inst Philadelphia PA 19104 USA MRC Mol Biol Lab Cambridge CB2 2QH England Duke Univ Med Ctr Dept Cell Biol Durham NC 27710 USA Max Planck Inst Med Forsch Biophys Abt D-69120 Heidelberg Germany

Motor actions of myosin were directly visualized by electron tomography of insect flight muscle quick-frozen during contraction. In 3D images, active crossbridges are usually single myosin heads, bound preferentially to actin target zones sited midway between troponins. Active attached bridges (similar to 30% of all heads) depart markedly in axial and azimuthal angles from Rayment's rigor acto-S1 model, one-third requiring motor domain (MD) tilting on actin, and two-thirds keeping rigor contact with actin while the light chain domain (LCD) tilts axially from similar to 105 degrees to similar to 70 degrees. The results suggest the MD tilts and slews on actin from weak to strong binding, followed by swinging of the LCD through an similar to 35 degrees axial angle, giving an similar to 13 nm interaction distance and an similar to 4-6 nm working stroke.

关键词： Actins/metabolism Animals Calcium Flight, Animal Flight, Animal Freezing Hemiptera/physiology image processing, computer-assisted/methods Microscopy, Electron/methods Models, Biological Muscle Contraction/physiology Muscle Fibers, Skeletal/metabolism Muscle Fibers, Skeletal/physiology Muscle Fibers, Skeletal/ultrastructure Myosin Light Chains/metabolism Time Factors Tomography/methods Troponin/metabolism

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Five-dimensional neuroimaging: Localization of the time-frequency dynamics of cortical activity

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NEUROimage 2008年第4期40卷 1686-1700页

作者： Dalal, Sarang S. Guggisberg, Adrian G. Edwards, Erik Sekihara, Kensuke Findlay, Anne M. Canolty, Ryan T. Berger, Mitchel S. Knight, Robert T. Barbaro, Nicholas M. Kirsch, Heidi E. Nagarajana, Srikantan S. Univ Calif San Francisco Dept Radiol Biomagnet Imaging Lab San Francisco CA 94143 USA Univ Calif Berkeley Helen Wills Neurosci Inst Berkeley CA 94720 USA Univ Calif San Francisco Joint Grad Grp Bioengn San Francisco CA 94143 USA Univ Calif San Francisco Dept Neurol Surg San Francisco CA 94143 USA Univ Calif San Francisco Dept Neurol San Francisco CA 94143 USA Univ Calif Berkeley Dept Psychol Berkeley CA 94720 USA Tokyo Metropolitan Univ Dept Syst Design & Engn Tokyo 1910065 Japan Univ Bern Inselspital Dept Neurol CH-3010 Bern Switzerland

The spatiotemporal dynamics of cortical oscillations across human brain regions remain poorly understood because of a lack of adequately validated methods for reconstructing such activity from noninvasive electrophysiological data. In this paper, we present a novel adaptive spatial filtering algorithm optimized for robust source time frequency reconstruction from magnetoencephalography (MEG) and electroencephalography ( EEG) data. The efficacy of the method is demonstrated with simulated sources and is also applied to real MEG data from a self-paced finger movement task. The algorithm reliably reveals modulations both in the beta band (12-30 Hz) and high gamma band (65-90 Hz) in sensorimotor cortex. The performance is validated by both across-subjects statistical comparisons and by intracranial electrocorticography (ECoG) data from two epilepsy patients. Interestingly, we also reliably observed high frequency activity (30-300 Hz) in the cerebellum, although with variable locations and frequencies across subjects. The proposed algorithm is highly parallelizable and runs efficiently on modern high-performance computing clusters. This method enables the ultimate promise of MEG and EEG for five-dimensional imaging of space, time, and frequency activity in the brain and renders it applicable for widespread studies of human cortical dynamics during cognition. (c) 2008 Elsevier Inc. All rights reserved.

关键词： Adult Algorithms Beta Rhythm Beta Rhythm Cerebellum/anatomy & histology Cerebellum/physiology Cerebral Cortex/anatomy & histology Cerebral Cortex/physiology Data Interpretation, Statistical Electroencephalography Electrophysiology Female Fingers/innervation Fingers/physiology Humans image processing, computer-assisted/methods Magnetoencephalography Magnetoencephalography Male Motor Cortex/anatomy & histology Motor Cortex/physiology Psychomotor Performance/physiology Somatosensory Cortex/anatomy & histology Somatosensory Cortex/physiology

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Superresolution Imaging of Chemical Synapses in the Brain

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NEURON 2010年第5期68卷 843-856页

作者： Dani, Adish Huang, Bo Bergan, Joseph Dulac, Catherine Zhuang, Xiaowei Harvard Univ Howard Hughes Med Inst Cambridge MA 02138 USA Harvard Univ Dept Mol & Cellular Biol Cambridge MA 02138 USA Harvard Univ Dept Phys Dept Chem & Chem Biol Cambridge MA 02138 USA

Determination of the molecular architecture of synapses requires nanoscopic image resolution and specific molecular recognition, a task that has so far defied many conventional imaging approaches. Here, we present a superresolution fluorescence imaging method to visualize the molecular architecture of synapses in the brain. Using multicolor, three-dimensional stochastic optical reconstruction microscopy, the distributions of synaptic proteins can be measured with nanometer precision. Furthermore, the wide-field, volumetric imaging method enables high-throughput, quantitative analysis of a large number of synapses from different brain regions. To demonstrate the capabilities of this approach, we have determined the organization of ten protein components of the presynaptic active zone and the postsynaptic density. Variations in synapse morphology, neurotransmitter receptor composition, and receptor distribution were observed both among synapses and across different brain regions. Combination with optogenetics further allowed molecular events associated with synaptic plasticity to be resolved at the single-synapse level.

关键词： Animals Brain/metabolism Brain/ultrastructure Brain Chemistry/physiology image processing, computer-assisted/instrumentation image processing, computer-assisted/methods Imaging, Three-Dimensional/instrumentation Imaging, Three-Dimensional/methods Immunohistochemistry/methods Immunohistochemistry/methods Mice Mice, Inbred C57BL Microchemistry/methods Microscopy, Fluorescence/instrumentation Microscopy, Fluorescence/methods Molecular Imaging/instrumentation Molecular Imaging/methods Nanotechnology Nerve Tissue Proteins/metabolism Nerve Tissue Proteins/ultrastructure Neuronal Plasticity/physiology Photomicrography/instrumentation Photomicrography/methods Presynaptic Terminals/metabolism Presynaptic Terminals/ultrastructure Stochastic Processes Synapses/metabolism Synapses/ultrastructure

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