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Linked independent component analysis for multimodal data fusion

NEUROimage 2011年第3期54卷 2198-2217页

作者： Groves, Adrian R. Beckmann, Christian F. Smith, Steve M. Woolrich, Mark W. Univ Oxford FMRIB Ctr Funct MRI Brain Dept Clin Neurol Oxford OX1 2JD England Radboud Univ Nijmegen Donders Inst Brain Cognit & Behav Ctr Cognit Neuroimaging Nijmegen Netherlands Univ Twente MIRA Inst Biomed Technol & Tech Med Enschede Netherlands Univ Oxford OHBA Ctr Human Brain Act Dept Psychiat Oxford OX1 2JD England

In recent years, neuroimaging studies have increasingly been acquiring multiple modalities of data and searching for task-or disease-related changes in each modality separately. A major challenge in analysis is to find systematic approaches for fusing these differing data types together to automatically find patterns of related changes across multiple modalities, when they exist. Independent Component Analysis (ICA) is a popular unsupervised learning method that can be used to find the modes of variation in neuroimaging data across a group of subjects. When multimodal data is acquired for the subjects, ICA is typically performed separately on each modality, leading to incompatible decompositions across modalities. Using a modular Bayesian framework, we develop a novel "Linked ICA" model for simultaneously modelling and discovering common features across multiple modalities, which can potentially have completely different units, signal- and contrast-to-noise ratios, voxel counts, spatial smoothnesses and intensity distributions. Furthermore, this general model can be configured to allow tensor ICA or spatially-concatenated ICA decompositions, or a combination of both at the same time. Linked ICA automatically determines the optimal weighting of each modality, and also can detect single-modality structured components when present. This is a fully probabilistic approach, implemented using Variational Bayes. We evaluate the method on simulated multimodal data sets, as well as on a real data set of Alzheimer's patients and age-matched controls that combines two very different types of structural MRI data: morphological data (grey matter density) and diffusion data (fractional anisotropy, mean diffusivity, and tensor mode). (C) 2010 Elsevier Inc. All rights reserved.

关键词： Algorithms Alzheimer Disease/pathology Anisotropy Bayes Theorem Brain/pathology Data Interpretation, Statistical Diffusion Tensor Imaging Diffusion Tensor Imaging Humans image processing, computer-assisted/methods Models, Neurological Models, Statistical Principal Component Analysis

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The influence of scoring method on variability in results obtained with the comet assay

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MUTAGENESIS 2011年第3期26卷 393-399页

作者： Azqueta, Amaya Meier, Silja Priestley, Catherine Gutzkow, Kristine Bjerve Brunborg, Gunnar Sallette, Jerome Soussaline, Francoise Collins, Andrew Univ Oslo Dept Nutr Fac Med N-0316 Oslo Norway AstraZeneca Res Dev Safety Assessment Macclesfield SK104TG Cheshire England Norwegian Inst Publ Hlth Div Environm Med Dept Chem Toxicol N-0403 Oslo Norway IMSTAR SA F-75006 Paris France

As part of a project to develop high throughput versions of the comet assay (single cell gel electrophoresis), with a consequent need for more efficient scoring, we have compared the performance of visual scoring, automated and semi-automated image analysis when assessing comets in the same set of gels from dose-response experiments with typical DNA-damaging agents. Human lymphoblastoid TK-6 cells were treated with concentrations of methylmethanesulphonate between 0.04 and 0.6 mM, and peripheral human lymphocytes were incubated, after embedding in agarose, with H(2)O(2) concentrations from 2.5 to 160 mu M. All three scoring methods proved capable of detecting a significant level of damage at the lowest concentration of each agent. Visual scoring systematically overestimates low levels of damage compared with computerised image analysis;on the other hand, heavily damaged comets are less efficiently detected with image analysis. Overall, the degree of agreement between the scoring methods is within acceptable limits according to a Bland-Altman analysis.

关键词： Cell Line Comet Assay/methods Comet Assay/standards Humans Hydrogen Peroxide/toxicity image processing, computer-assisted/methods Lymphocytes/drug effects Methyl Methanesulfonate/toxicity Research Design/statistics & numerical data

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Predicting subject-driven actions and sensory experience in a virtual world with Relevance Vector Machine Regression of fMRI data

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NEUROimage 2011年第2期56卷 651-661页

作者： Valente, Giancarlo De Martino, Federico Esposito, Fabrizio Goebel, Rainer Formisano, Elia Univ Maastricht Dept Cognit Neurosci Maastricht Brain Imaging Ctr NL-6200 MD Maastricht Netherlands

In this work we illustrate the approach of the Maastricht Brain Imaging Center to the PBAIC 2007 competition, where participants had to predict, based on fMRI measurements of brain activity, subject driven actions and sensory experience in a virtual world. After standard pre-processing (slice scan time correction, motion correction), we generated rating predictions based on linear Relevance Vector Machine (RVM) learning from all brain voxels. Spatial and temporal filtering of the time series was optimized rating by rating. For some of the ratings (e.g. Instructions, Hits, Faces, Velocity), linear RVM regression was accurate and very consistent within and between subjects. For other ratings (e.g. Arousal, Valence) results were less satisfactory. Our approach ranked overall second. To investigate the role of different brain regions in ratings prediction we generated predictive maps, i.e. maps of the weighted contribution of each voxel to the predicted rating. These maps generally included (but were not limited to) "specialized" regions which are consistent with results from conventional neuroimaging studies and known functional neuroanatomy. In conclusion, Sparse Bayesian Learning models, such as RVM, appear to be a valuable approach to the multivariate regression of fMRI time series. The implementation of the Automatic Relevance Determination criterion is particularly suitable and provides a good generalization, despite the limited number of samples which is typically available in fMRI. Predictive maps allow disclosing multi-voxel patterns of brain activity that predict perceptual and behavioral subjective experience. (C) 2010 Elsevier Inc. All rights reserved.

关键词： Artificial Intelligence Brain/physiology Brain Mapping/methods Brain Mapping/methods Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Pattern Recognition, Automated/methods

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Pain is associated with regional grey matter reduction in the general population

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PAIN 2011年第4期152卷 904-911页

作者： Ruscheweyh, Ruth Deppe, Michael Lohmann, Hubertus Stehling, Christoph Floeel, Agnes Ringelstein, E. Bernd Knecht, Stefan Univ Munster Dept Neurol D-48129 Munster Germany Univ Munster Inst Clin Radiol D-48129 Munster Germany Charite Dept Neurol D-13353 Berlin Germany

Regional decreases in grey matter volume as detected by magnetic resonance imaging-based volumetry have been reported in several clinical chronic pain cohorts. Here, we used voxel-based morphometry in a nonclinical cohort to investigate whether grey matter alterations also occur in older individuals (aged 40-85 years) from the general population. Based on self-report of pain, we identified 31 pain-free controls, 45 subjects with ongoing pain (low back pain, headache, or lower extremity joint pain) who had at least moderate pain on more than 3 days/month, and 29 individuals with past pain (stopped for > 12 months). Relative to controls, the ongoing pain group showed regional grey matter volume decreases, predominantly in cingulate, prefrontal, and motor/premotor regions. No grey matter volume decreases were found in the group with pain that had stopped for > 12 months. These results show that pain-related grey matter volume decreases are present in individuals from the general population. The lack of morphometric anomalies in subjects with past pain supports recent evidence suggesting that pain-related grey matter changes are reversible after cessation of pain. (C) 2011 International Association for the Study of Pain. Published by Elsevier B.V. All rights reserved.

关键词： Aged Brain/pathology Brain Mapping Brain Mapping Female Humans image processing, computer-assisted/methods Magnetic Resonance Imaging/methods Male Middle Aged Pain/classification Pain/pathology Pain Measurement Pain Measurement Self Report

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Decoding the direction of auditory motion in blind humans

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NEUROimage 2011年第2期56卷 681-687页

作者： Wolbers, Thomas Zahorik, Pavel Giudice, Nicholas A. Univ Edinburgh Ctr Cognit & Neural Syst Edinburgh EH8 9JZ Midlothian Scotland Univ Edinburgh Ctr Cognit Ageing & Cognit Epidemiol Edinburgh EH8 9JZ Midlothian Scotland Univ Louisville Heuser Hearing Inst Dept Psychol & Brain Sci Louisville KY 40292 USA Univ Maine Dept Spatial Informat Sci & Engn Orono ME 04469 USA

Accurate processing of nonvisual stimuli is fundamental to humans with visual impairments. In this population, moving sounds activate an occipito-temporal region thought to encompass the equivalent of monkey area MT+, but it remains unclear whether the signal carries information beyond the mere presence of motion. To address this important question, we tested whether the processing in this region retains functional properties that are critical for accurate motion processing and that are well established in the visual modality. Specifically, we focussed on the property of 'directional selectivity', because MT+ neurons in non-human primates fire preferentially to specific directions of visual motion. Recent neuroimaging studies have revealed similar properties in sighted humans by successfully decoding different directions of visual motion from fMRI activation patterns. Here we used fMRI and multivariate pattern classification to demonstrate that the direction in which a sound is moving can be reliably decoded from dorsal occipito-temporal activation in the blind. We also show that classification performance is at chance (i) in a control region in posterior parietal cortex and (ii) when motion information is removed and subjects only hear a sequence of static sounds presented at the same start and end positions. These findings reveal that information about the direction of auditory motion is present in dorsal occipito-temporal responses of blind humans. As such, this area, which appears consistent with the hMT+ complex in the sighted, provides crucial information for the generation of a veridical percept of moving non-visual stimuli. (C) 2010 Elsevier Inc. All rights reserved.

关键词： Adult Auditory Perception/physiology Blindness Brain Mapping/methods Brain Mapping/methods Cerebral Cortex/physiology Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Male Middle Aged Movement/physiology Visually Impaired Persons

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FISH Finder: a high-throughput tool for analyzing FISH images

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BIOINFORMATICS 2011年第7期27卷 933-938页

作者： Shirley, James W. Ty, Sereyvathana Takebayashi, Shin-ichiro Liu, Xiuwen Gilbert, David M. Florida State Univ Dept Biol Sci Tallahassee FL 32306 USA Florida State Univ Dept Comp Sci Tallahassee FL 32306 USA

Motivation: Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus. Analyzing the data from FISH images is a tedious process that invokes an element of subjectivity. Automated FISH image analysis offers savings in time as well as gaining the benefit of objective data analysis. While several FISH image analysis software tools have been developed, they often use a threshold- based segmentation algorithm for nucleus segmentation. As fluorescence signal intensities can vary significantly from experiment to experiment, from cell to cell, and within a cell, threshold- based segmentation is inflexible and often insufficient for automatic image analysis, leading to additional manual segmentation and potential subjective bias. To overcome these problems, we developed a graphical software tool called FISH Finder to automatically analyze FISH images that vary significantly. By posing the nucleus segmentation as a classification problem, compound Bayesian classifier is employed so that contextual information is utilized, resulting in reliable classification and boundary extraction. This makes it possible to analyze FISH images efficiently and objectively without adjustment of input parameters. Additionally, FISH Finder was designed to analyze the distances between differentially stained FISH probes.

关键词： Animals Bayes Theorem Cell Nucleus/chemistry computer Graphics Humans image processing, computer-assisted/methods In Situ Hybridization, Fluorescence/methods In Situ Hybridization, Fluorescence/methods Mice Microscopy, Fluorescence Software

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Testing the ICA mixing matrix based on inter-subject or inter-session consistency

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NEUROimage 2011年第1期58卷 122-136页

作者： Hyvarinen, Aapo Univ Helsinki Dept Comp Sci HUUT Dept Math & Stat FIN-00014 Helsinki Finland Univ Helsinki Dept Psychol FIN-00014 Helsinki Finland

Independent component analysis (ICA) is increasingly used for analyzing brain imaging data. ICA typically gives a large number of components, many of which may be just random, due to insufficient sample size, violations of the model, or algorithmic problems. Few methods are available for computing the statistical significance (reliability) of the components. We propose to approach this problem by performing ICA separately on a number of subjects, and finding components which are sufficiently consistent (similar) over subjects. Similarity is defined here as the similarity of the mixing coefficients, which usually correspond to spatial patterns in EEG and MEG. The threshold of what is "sufficient" is rigorously defined by a null hypothesis under which the independent components are random orthogonal components in the whitened space. Components which are consistent in different subjects are found by clustering under the constraint that a cluster can only contain one source from each subject, and by constraining the number of the false positives based on the null hypothesis. Instead of different subjects, the method can also be applied on different recording sessions from a single subject. The testing method is particularly applicable to EEG and MEG analysis. (C) 2011 Elsevier Inc. All rights reserved.

关键词： Adult Algorithms Artifacts Cluster Analysis computer Simulation Data Interpretation, Statistical Electroencephalography/methods False Positive Reactions Fourier Analysis Fourier Analysis Humans image processing, computer-assisted/methods Individuality Magnetoencephalography/methods Magnetoencephalography/methods Male Middle Aged Principal Component Analysis

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Automated scoring of lymphocyte micronuclei by the MetaSystems Metafer image cytometry system and its application in studies of human mutagen sensitivity and biodosimetry of genotoxin exposure

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MUTAGENESIS 2011年第1期26卷 169-175页

作者： Rossnerova, Andrea Spatova, Milada Schunck, Christian Sram, Radim J. Acad Sci Czech Republ Inst Expt Med Dept Genet Ecotoxicol Vvi Prague 14220 4 Czech Republic MetaSyst GmbH D-68804 Altlussheim Germany

Automated image analysis scoring of micronuclei (MN) in cells can facilitate the objective and rapid measurement of genetic damage in mammalian and human cells. This approach was repeatedly developed and tested over the past two decades but none of the systems were sufficiently robust for routine analysis of MN until recently. New methodological, hardware and software developments have now allowed more advanced systems to become available. This mini-review presents the current stage of development and validation of the Metasystems Metafer MNScore system for automated image analysis scoring of MN in cytokinesis-blocked binucleated lymphocytes, which is the best-established method for studying MN formation in humans. The results and experience of users of this system from 2004 until today are reviewed in this paper. Significant achievements in the application of this method in research related to mutagen sensitivity phenotype in cancer risk, radiation biodosimetry and biomonitoring studies of air pollution (enriched by new data) are described. Advantages as well as limitations of automated image analysis in comparison with traditional visual analysis are discussed. The current increased use of the Metasystems Metafer MNScore system in various studies and the growing number of publications based on automated image analysis scoring of MN is promising for the ongoing and future application of this approach.

关键词： Adolescent Adult Aged Child Child, Preschool Dose-Response Relationship, Drug Humans image Cytometry/methods image Cytometry/methods image processing, computer-assisted/methods Infant Infant, Newborn Lymphocyte Count/methods Lymphocyte Count/methods Lymphocytes/drug effects Lymphocytes/ultrastructure Micronuclei, Chromosome-Defective Micronucleus Tests/instrumentation Middle Aged Mutagens/toxicity Young Adult

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Improved detectability and signal strength for rotating phase fluorescence immunoassays through image processing

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ANALYST 2011年第2期136卷 365-373页

作者： Mahanti, Prasun Taylor, Thomas Hayes, Mark A. Cochran, Douglas Petkus, Matthew M. Arizona State Univ Tempe AZ 85287 USA

Fluorescence immunoassays based on rotating solid phase have shown promise of lowered detection limits, among other advantages. However, intrinsic background distortion effects have limited their utility. Here, novel image processing strategies are used to minimize these effects and improve the estimate of concentration and lower the detection limit. This initial demonstration of a new processing capability is performed on data for a protein, myoglobin, which is a biomarker for acute myocardial infarction. For these data, compared with published results, the detection limit is improved by a factor of approximately one hundred (to 700 fM), which is competitive with or better than other immunoassay strategies (ELISA, for example) that are fully developed. This work suggests that image and video processing technologies can provide a valuable alternative approach to biochemical detection and concentration estimation.

关键词： Algorithms Animals Equipment Design Fluorescence Fluorescence Horses image processing, computer-assisted/methods Immunoassay/instrumentation Immunoassay/instrumentation Immunoassay/methods Immunoassay/methods Myoglobin/analysis Sensitivity and Specificity

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Modeling and analysis of mechanisms underlying fMRI-based decoding of information conveyed in cortical columns

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NEUROimage 2011年第2期56卷 627-642页

作者： Chaimow, Denis Yacoub, Essa Ugurbil, Kamil Shmuel, Amir McGill Univ Montreal Neurol Inst Dept Neurol & Neurosurg Montreal PQ H3A 2B4 Canada McGill Univ Montreal Neurol Inst Dept Biomed Engn Montreal PQ H3A 2B4 Canada Max Planck Inst Biol Cybernet Tubingen Germany Univ Minnesota Sch Med Ctr MR Res Minneapolis MN 55455 USA

Multivariate machine learning algorithms applied to human functional MRI (fMRI) data can decode information conveyed by cortical columns, despite the voxel-size being large relative to the width of columns. Several mechanisms have been proposed to underlie decoding of stimulus orientation or the stimulated eye. These include: (I) aliasing of high spatial-frequency components, including the main frequency component of the columnar organization, (II) contributions from local irregularities in the columnar organization, (III) contributions from large-scale non-columnar organizations, (IV) functionally selective veins with biased draining regions, and (V) complex spatio-temporal filtering of neuronal activity by fMRI voxels. Here we sought to assess the plausibility of two of the suggested mechanisms: (I) aliasing and (II) local irregularities, using a naive model of BOLD as blurring and MRI voxel sampling. To this end, we formulated a mathematical model that encompasses both the processes of imaging ocular dominance (OD) columns and the subsequent linear classification analysis. Through numerical simulations of the model, we evaluated the distribution of functional differential contrasts that can be expected when considering the pattern of cortical columns, the hemodynamic point spread function, the voxel size, and the noise. We found that with data acquisition parameters used at 3 Tesla, sub-voxel supra-Nyquist frequencies, including frequencies near the main frequency of the OD organization (0.5 cycles per mm), cannot contribute to the differential contrast. The differential functional contrast of local origin is dominated by low-amplitude contributions from low frequencies, associated with irregularities of the cortical pattern. Realizations of the model with parameters that reflected best-case scenario and the reported BOLD point-spread at 3 Tesla (3.5 mm) predicted decoding performances lower than those that have been previously obtained at this magnetic field str

关键词： Brain Mapping/methods Brain Mapping/methods Cerebral Cortex/physiology Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Models, Neurological Models, Theoretical

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