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Evaluation of volume-based and surface-based brain image registration methods

NEUROimage 2010年第1期51卷 214-220页

作者： Klein, Arno Ghosh, Satrajit S. Avants, Brian Yeo, B. T. T. Fischl, Bruce Ardekani, Babak Gee, James C. Mann, J. J. Parsey, Ramin V. Columbia Univ New York State Psychiat Inst New York NY 10032 USA MIT Elect Res Lab Cambridge MA 02139 USA Univ Penn Dept Radiol Penn Image Comp & Sci Lab Philadelphia PA 19104 USA Harvard Univ Cognit Neurosci Lab Cambridge MA 02138 USA Massachusetts Gen Hosp Athinoula A Martinos Ctr Boston MA 02114 USA Harvard Univ Sch Med Dept Radiol Cambridge MA 02138 USA MIT CSAIL Cambridge MA 02139 USA Nathan S Kline Inst Psychiat Res Orangeburg NY 10962 USA NYU Sch Med New York NY 10016 USA

Establishing correspondences across brains for the purposes of comparison and group analysis is almost universally done by registering images to one another either directly or via a template. However, there are many registration algorithms to choose from. A recent evaluation of fully automated nonlinear deformation methods applied to brain image registration was restricted to volume-based methods. The present study is the first that directly compares some of the most accurate of these volume registration methods with surface registration methods, as well as the first study to compare registrations of whole-head and brain-only (de-skulled) images. We used permutation tests to compare the overlap or Hausdorff distance performance for more than 16,000 registrations between 80 manually labeled brain images. We compared every combination of volume-based and surface-based labels, registration, and evaluation. Our primary findings are the following: 1. de-skulling aids volume registration methods;2. custom-made optimal average templates improve registration over direct pairwise registration;and 3. resampling volume labels on surfaces or converting surface labels to volumes introduces distortions that preclude a fair comparison between the highest ranking volume and surface registration methods using present resampling methods. From the results of this study, we recommend constructing a custom template from a limited sample drawn from the same or a similar representative population, using the same algorithm used for registering brains to the template. (C) 2010 Published by Elsevier Inc.

关键词： Adult Algorithms Brain/anatomy & histology Female Head/anatomy & histology Humans image processing, computer-assisted/methods Imaging, Three-Dimensional/methods Magnetic Resonance Imaging/methods Male Organ Size Software Young Adult

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A computer-assisted image-processing METHOD FOR DETERMINING RELATIVE CARDIAC-FUNCTION IN THE CHICK-EMBRYO

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TERATOLOGY 1991年第6期44卷 641-651页

作者： BRUYERE, HJ XU, B JAMES, TL MAGEE, MJ University of Wyoming Laramie 82071.

The general objective of this study was to develop a noninvasive method for efficiently and reproducibly determining relative cardiac function parameters in the chick embryo. The specific objectives of the study were 1) to develop several methods for computer-assisted image processing and quantitation of relative intraventricular blood volumes in the 3-day-old embryonic chick heart and 2) to compare methods for precision and with a previously established manual processing method. images of the embryonic chick heart in ovo were recorded on videocassette tape, digitized, and enhanced by computer-aided histogram equalization. The area occupied by blood within the common ventricle was extracted by region-growing and spurious region removal algorithms and defined by the determination of edge-pixel coordinates. Edge-pixel coordinates of the longitudinal and transverse axes of the common ventricular blood region were located by three different methods, the lengths of the axes calculated, and volumes computed from the equation for determining volume of a prolate spheroid. Twenty-five images of the embryonic heart were randomly selected and processed. Volumes were calculated with each of the three methods on six different occasions. A coefficient of variation was determined for each image by each of the three methods. A mean coefficient of variation was calculated for each method. The intraobserver mean coefficient of variation for each method was 7.4%. When a 2-way ANOVA was conducted, mean coefficients of variation did not differ significantly for the three methods. However, computer processing (in addition to significantly reducing the time required to generate data) reduced the coefficient of variation observed in manual processing by 56.5%.

关键词： Analysis of Variance Animals Blood Volume Chick Embryo Heart/embryology Heart Function Tests/methods image processing, computer-assisted/methods Reproducibility of Results

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Lattice parameters from direct-space images at two tilts

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ULTRAMICROSCOPY 2003年第3-4期94卷 245-262页

作者： Qin, W Fraundorf, P Univ Missouri Ctr Mol Elect St Louis MO 63121 USA

Lattices in three dimensions are oft studied from the "reciprocal space" perspective of diffraction. Today, the full lattice of a crystal can often be inferred from direct-space information about three sets of non-parallel lattice planes. Such data can come from electron-phase (or less easily Z contrast images) taken at two tilts, provided that one image shows two non-parallel lattice periodicities, and the other shows a periodicity not coplanar with the first two. We outline here protocols for measuring the 3D parameters of cubic lattice types in this way. For randomly oriented nanocrystals with cell side greater than twice the continuous transfer limit, orthogonal +/- 15degrees and +/- 10degrees tilt ranges might allow one to measure 3D parameters of all such lattice types in a specimen from only two well-chosen images. The strategy is illustrated by measuring the lattice parameters of a 10 nm WC1-x crystal in a plasma-enhanced chemical-vapor deposited thin film. (C) 2002 Elsevier Science B.V. All rights reserved.

关键词： Algorithms Crystallization/methods image processing, computer-assisted/methods Microscopy, Electron/methods Research Design/statistics & numerical data

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PHOELIX - A PACKAGE FOR SEMIAUTOMATED HELICAL RECONSTRUCTION

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ULTRAMICROSCOPY 1995年第3-4期58卷 245-259页

作者： WHITTAKER, M CARRAGHER, BO MILLIGAN, RA UNIV ILLINOIS BECKMAN INST URBANA IL 61801 USA UNIV ILLINOIS DEPT CELL & STRUCT BIOL URBANA IL 61801 USA

We describe a set of procedures and algorithms which have been developed to provide an efficient and reliable method for reconstructing a three-dimensional density map from specimens with helical symmetry. These procedures build on the original MRC helical processing suite, with extensions principally developed using the SUPRIM image processing package. Actomyosin is used as a model specimen to demonstrate the utility of this repackaged and expanded set of routines. The time required to complete a three-dimensional map has been reduced from several weeks using traditional manual techniques to a few days. The increased signal/noise provided has allowed for the extraction of additional layer lines not previously identified by manual techniques.

关键词： Actomyosin/chemistry Algorithms image processing, computer-assisted/methods Molecular Conformation Reproducibility of Results Time Factors

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Software for quantification of labeled bacteria from digital microscope images by automated image analysis

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BIOTECHNIQUES 2005年第6期39卷 859-863页

作者： Selinummi, J Seppälä, J Yli-Harja, O Puhakka, JA Tampere Univ Technol Inst Signal Proc FIN-33101 Tampere Finland

Automated image analysis software, CellC, was developed and validated for quantification of bacterial cells from digital microscope images. CellC enables automated enumeration of bacterial cells, comparison of total count and specific count images [e.g., 4',6-diamino-2-phenylindole (DAPI) and fluorescence in situ hybridization (FISH) images], and provides quantitative estimates of cell morphology. The software includes an intuitive graphical user interface that enables easy usage as well. as sequential analysis of multiple images without user intervention. Validation of enumeration reveals correlation to be better than 0.98 when total bacterial counts by CellC are compared with manual enumeration, with all validated image types. The software is freely available and modifiable: the executable files and MATLAB(R) source codes can be obtained at ***/sgn/csb/cellc.

关键词： Bioreactors Colony Count, Microbial/methods Colony Count, Microbial/methods image processing, computer-assisted/methods Microscopy Software

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computer-CONTROLLED SPOT-SCAN IMAGING OF CROTOXIN COMPLEX-CRYSTALS WITH 400 KEV ELECTRONS AT NEAR-ATOMIC RESOLUTION

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ULTRAMICROSCOPY 1992年第1-4期46卷 229-240页

作者： BRINK, J CHIU, W DOUGHERTY, M W.M. Keck Center for Computational Biology Verna and Marrs McLean Department of Biochemistry Baylor College of Medicine Houston TX 77030.

400 keV electrons yield a better relative image contrast than 100 keV electrons for a beam-sensitive organic crystal when spot-scan imaging is used [J. Brink and W. Chiu, J. Microscopy 161 (1991) 279]. A FORTRAN 77 program has been written to operate the spot-scan imaging system on a computer workstation under the VMS operating system which is interfaced serially to the JEOL4000 electron microscope. We demonstrate the application of this implementation by imaging crotoxin complex crystals embedded in either vitreous ice or glucose to 2.5 angstrom resolution. The intensity strength of the structure factors of this protein crystal are different at low ( > 10 angstrom) resolution but similar at high resolution ( < 10 angstrom) for the two embedding media as expected from their scattering contrast difference. Based on our experience as judged from the electron diffraction patterns of highly tilted crystals, flat crystals embedded in glucose can be readily obtained. Furthermore, our spot-scan imaging system also has the option of correcting the focus gradient that is present in images of tilted specimens.

关键词： computers Crotoxin image processing, computer-assisted/instrumentation image processing, computer-assisted/methods Microscopy, Electron, Scanning Transmission/instrumentation Microscopy, Electron, Scanning Transmission/methods Software

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USE OF RADIAL DENSITY PLOTS TO CALIBRATE image MAGNIFICATION FOR FROZEN-HYDRATED SPECIMENS

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ULTRAMICROSCOPY 1993年第3期48卷 347-358页

作者： BELNAP, DM GROCHULSKI, WD OLSON, NH BAKER, TS PURDUE UNIV DEPT BIOL SCIW LAFAYETTEIN 47907

Accurate magnification calibration for transmission electron microscopy is best achieved with the use of appropriate standards and an objective calibration technique. We have developed a reliable method for calibrating the magnification of images from frozen-hydrated specimens. Invariant features in radial density plots of a standard are compared with the corresponding features in a ''defocused'' X-ray model of the same standard. Defocused X-ray models were generated to mimic the conditions of cryo-electron microscopy. The technique is demonstrated with polyoma virus, which was used as an internal standard to calibrate micrographs of bovine papilloma virus type 1 and bacteriophage PHIX174. Calibrations of the micrographs were estimated to be accurate to 0.35%-0.5%. Accurate scaling of a three-dimensional structure allows additional calibrations to be made with radial density plots computed from two- or three-dimensional data.

关键词： Bacteriophages/ultrastructure Calibration/standards Cryopreservation Cryopreservation image processing, computer-assisted/methods Microscopy, Electron/methods Papillomaviridae/ultrastructure Polyomaviridae Reference Standards

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Characterizing the spatio-temporal behavior of cell populations through image autoand cross-correlation microscopy

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BIOTECHNIQUES 2007年第1期43卷 107-115页

作者： Bonnet, Noeel Delavoie, Franck Zahm, Jean-Marie Univ Reims UMR 514 INSERM U514 F-51092 Reims France

We propose two methods for characterizing the spatio-temporal behavior of cell populations in culture. The first method, image auto-correlation microscopy (IACM), allows us to characterize the variation in the number of objects as a function of time, thus enabling the quantification of the clustering properties of cell populations to be performed. The second method, image crosscorrelation microscopy (ICCM), allows us to characterize the migration properties of cell populations. The latter method does not require estimation or measurement of the trajectories of individual cells, which is very demanding when populations of >100 cells are examined. The capabilities of the two methods are demonstrated with simulated cell populations, and their usefulness is illustrated with experiments involving invasive and noninvasive tumor cell populations.

关键词： Animals Catechin/analogs & derivatives Catechin/pharmacology Cell Aggregation/drug effects Cell Line Cell Movement/drug effects Cell Survival/drug effects Cells/cytology computer Simulation Humans image processing, computer-assisted/methods Mice Microscopy/methods Neoplasms/pathology Time Factors

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DOUBLE-TILT ELECTRON TOMOGRAPHY

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ULTRAMICROSCOPY 1995年第3期60卷 393-410页

作者： PENCZEK, P MARKO, M BUTTLE, K FRANK, J NEW YORK STATE DEPT HLTH WADSWORTH CTR LABS & RESALBANYNY 12201

Fidelity of tomographic reconstructions is improved and reconstruction artifacts are reduced, without increasing the number of projections, by combining tilt series taken around two orthogonal axes. Test reconstructions were made from high-voltage EM of rat liver mitochondria in a 0.6 mu m thick plastic section. A number of schemes for selecting tilt angles for the projections are compared. A new method for aligning fiducial markers is described. It uses an iterative algorithm to determine the shift, scale, in-plane rotation and tilt angle for each tilt image, enforcing agreement of the expected locations of the fiducial markers in 3D space. These 3D locations are used to find the orientation between two tilt series acid to both sets of projections.

关键词： Animals image processing, computer-assisted/methods Mitochondria, Liver/ultrastructure Rats Tomography/methods

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TEM based high resolution and low-dose scanning electron nanodiffraction technique for nanostructure imaging and analysis

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MICRON 2015年 71卷 39-45页

作者： Kim, Kyou-Hyun Xing, Hui Zuo, Jian-Min Zhang, Peng Wang, Haifeng Univ Illinois Dept Mat Sci & Engn Urbana IL 61801 USA Univ Illinois Frederick Seitz Mat Res Lab Urbana IL 61801 USA Shanghai Jiao Tong Univ Sch Mat Sci & Engn Shanghai 200240 Peoples R China Western Digital Technol Inc Fremont CA 94539 USA

We report a high resolution and low-dose scanning electron nanodiffraction (SEND) technique for nanostructure analysis. The SEND patterns are recorded in a transmission electron microscope (TEM) using a low-brightness similar to 2 nm electron beam with a LaB6 thermionic source obtained by a large demagnification of the condenser 1 lens. The diffraction pattern is directly recorded using a CCD camera optimized for low-dose imaging. A custom script was developed for calibration and automated data acquisition. The performance of low-dose SEND is evaluated using nanostructured Au as a test sample for the quality of diffraction patterns, sample stability and probe size. We demonstrate that our method provides an effective and robust way for recording diffraction patterns from nanometer-sized grains. (C) 2015 Elsevier Ltd. All rights reserved.

关键词： Calibration Electrons Electrons Gold image processing, computer-assisted/methods Microscopy, Electron, Transmission/methods Nanostructures/analysis Nanostructures/ultrastructure

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