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Investigation of spatial resolution, partial volume effects and smoothing in functional MRI using artificial 3D time series

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NEUROimage 2008年第2期41卷 346-353页

作者： Weibull, A. Gustavsson, H. Mattsson, S. Svensson, J. Lund Univ Dept Med Radiat Phys SE-20502 Malmo Sweden Siemens Med Solut Malmo Sweden

This work addresses the balance between temporal signal-to-noise ratio (tSNR) and partial volume effects (PVE) in functional magnetic resonance imaging (fMRI) and investigates the impact of the choice of spatial resolution and smoothing. In fMRI, since physiological time courses are monitored, tSNR is of greater importance than image SNR. Improving SNR by an increase in voxel volume may be of negligible benefit when physiological fluctuations dominate the noise. Furthermore, at large voxel volumes, PVE are more pronounced, leading to an overall loss in performance. Artificial fMRI time series, based on high-resolution anatomical data, were used to simulate BOLD activation in a controlled manner. The performance was subsequently quantified as a measure of how well the resulted activation matched the simulated activation. The performance was highly dependent on the spatial resolution. At high contrast-to-noise ratio (CNR), the optimal voxel volume was small, i.e. in the region of 2(3) mm(3). It was also shown that using a substantially larger voxel volume in this case could potentially negate the CNR benefits. The optimal smoothing kernel width was dependent on the CNR, being larger at poor CNR. At CNR > 1, little or no smoothing proved advantageous. The use of artificial time series gave an opportunity to quantitatively investigate the effects of partial volume and smoothing in single subject fMRI. It was shown that a proper choice of spatial resolution and smoothing kernel width is important for fMRI performance. (c) 2008 Elsevier Inc. All rights reserved.

关键词： Artifacts Brain/physiology Female Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Models, Neurological

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Multi-atlas segmentation of the whole hippocampus and subfields using multiple automatically generated templates

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NEUROimage 2014年 101卷 494-512页

作者： Pipitone, Jon Park, Min Tae M. Winterburn, Julie Lett, Tristram A. Lerch, Jason P. Pruessner, Jens C. Lepage, Martin Voineskos, Aristotle N. Chakravarty, M. Mallar Ctr Addict & Mental Hlth Kimel Family Translat Imaging Genet Lab Toronto ON M5T 1R8 Canada Hosp Sick Children Neurosciences & Mental Hlth Lab Toronto ON M5G 1X8 Canada Univ Toronto Dept Med Biophys Toronto ON Canada Douglas Mental Hlth Univ Inst Verdun PQ Canada McGill Univ Dept Psychiat Montreal PQ Canada Univ Toronto Dept Psychiat Toronto ON Canada Univ Toronto Inst Biomat & Biomed Engn Toronto ON Canada Baycrest Rotman Res Inst Toronto ON Canada Univ Toronto Inst Med Sci Toronto ON Canada

Introduction: Advances in image segmentation of magnetic resonance images (MRI) have demonstrated that multi-atlas approaches improve segmentation over regular atlas-based approaches. These approaches often rely on a large number of manually segmented atlases (e.g. 30-80) that take significant time and expertise to produce. We present an algorithm, MAGeT-Brain (Multiple Automatically Generated Templates), for the automatic segmentation of the hippocampus that minimises the number of atlases needed whilst still achieving similar agreement to multi-atlas approaches. Thus, our method acts as a reliable multi-atlas approach when using special or hard-to-define atlases that are laborious to construct. Method: MAGeT-Brain works by propagating atlas segmentations to a template library, formed from a subset of target images, via transformations estimated by nonlinear image registration. The resulting segmentations are then propagated to each target image and fused using a label fusion method. We conduct two separate Monte Carlo cross-validation experiments comparing MAGeT-Brain and basic multi-atlas whole hippocampal segmentation using differing atlas and template library sizes, and registration and label fusion methods. The first experiment is a 10-fold validation (per parameter setting) over 60 subjects taken from the Alzheimer's Disease Neuroimaging Database (ADNI), and the second is a five-fold validation over 81 subjects having had a first episode of psychosis. In both cases, automated segmentations are compared with manual segmentations following the Pruessner-protocol. Using the best settings found from these experiments, we segment 246 images of the ADNI1: Complete 1Yr 1.5T dataset and compare these with segmentations from existing automated and semi-automated methods: FSL FIRST, FreeSurfer, MAPER, and SNT. Finally, we conduct a leave-one-out cross-validation of hippocampal subfield segmentation in standard 3T T1-weighted images, using five high-resolution manually

关键词： Adolescent Adult Aged Aged, 80 and over Aging/pathology Alzheimer Disease/pathology Atlases as Topic Female Hippocampus/anatomy & histology Hippocampus/pathology Humans image processing, computer-assisted/methods image processing, computer-assisted/standards Magnetic Resonance Imaging/methods Magnetic Resonance Imaging/standards Male Middle Aged Monte Carlo Method Psychotic Disorders/pathology Young Adult

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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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Digital image processing for rapid analysis of differentially expressed transcripts on high-density cDNA arrays

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BIOTECHNIQUES 1999年第6期26卷 1174-+页

作者： Adryan, B Carlguth, V Decker, HJ Univ Mainz Med Clin 3 Dept Hematol Oncol Lab Tumorgenet & Mol Cytogenet D-55131 Mainz Germany

Usage of filter arrays is becoming increasingly attractive for many research laboratories involved indetermination of gene-expression profiles. However analysis of numerous spots, representing genes or partial gene sequences (ESTs), is still tedious work involving the ordered analysis of vast amounts of numerical tabular data. We present a vapid and efficient method for the visual identification of differentially expressed targets on high-density cDNA filter arrays using standard laboratory equipment and standard software, which is available for free. The method we introduce provides an inexpensive alternative, and no changes in the experimental set up are required. Our results were verified by densitometric analyses performed with an established system.

关键词： Autoradiography Autoradiography Cloning, Molecular/methods Color Densitometry/methods DNA, Complementary/analysis Gene Expression image processing, computer-assisted/methods Software Transcription, Genetic

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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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Dysmyelination revealed through MRI as increased radial (but unchanged axial) diffusion of water

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NEUROimage 2002年第3期17卷 1429-1436页

作者： Song, SK Sun, SW Ramsbottom, MJ Chang, C Russell, J Cross, AH Washington Univ Dept Chem St Louis MO 63110 USA Washington Univ Sch Med Biomed MR Lab St Louis MO 63110 USA Washington Univ Dept Radiol St Louis MO 63110 USA Washington Univ Dept Neurol St Louis MO 63110 USA Washington Univ Dept Pharmacol & Mol Biol St Louis MO 63110 USA Acad Sinica Inst Biomed Sci Taipei Taiwan Natl Yang Ming Univ Dept Biomed Engn Taipei Taiwan

Myelin loss and axonal damage are both observed in white matter injuries. Each may have significant impact on the long-term disability of patients. Currently, there does not exist a noninvasive biological marker that enables differentiation between myelin and axonal injury. We describe herein the use of magnetic resonance diffusion tensor imaging (DTI) to quantify the effect of dysmyelination on water directional diffusivities in brains of shiverer mice in vivo. The principal diffusion eigenvalues of eight axonal fiber tracts that can be identified with certainty on DTI maps were measured. The water diffusivity perpendicular to axonal fiber tracts, lambda(perpendicular to), was significantly higher in shiverer mice compared with age-matched controls, reflecting the lack of myelin and the increased freedom of cross-fiber diffusion in white matter. The water diffusivity parallel to axonal fiber tracts, lambda(parallel to), was not different, which is consistent with the presence of intact axons. It is clear that dysmyelination alone does not impact lambda(parallel to). The presence of intact axons in the setting of incomplete myelination was confirmed by electron microscopy. Although further validation is still needed, our finding suggests that changes in lambda(perpendicular to) and lambda(parallel to) may potentially be used to differentiate myelin loss versus axonal injury. (C) 2002 Elsevier Science (USA).

关键词： Animals Brain/pathology Brain Diseases/diagnosis Brain Diseases/pathology Diagnosis, Differential Diffuse Axonal Injury/diagnosis Diffuse Axonal Injury/diagnosis Diffuse Axonal Injury/pathology Diffuse Axonal Injury/pathology Diffusion Magnetic Resonance Imaging/methods Disease Models, Animal Hereditary Central Nervous System Demyelinating Diseases/diagnosis Hereditary Central Nervous System Demyelinating Diseases/diagnosis Hereditary Central Nervous System Demyelinating Diseases/pathology Hereditary Central Nervous System Demyelinating Diseases/pathology Heterozygote Homozygote Humans image processing, computer-assisted/methods Mice Mice, Neurologic Mutants Nerve Fibers, Myelinated/pathology

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A Bayesian framework for global tractography

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NEUROimage 2007年第1期37卷 116-129页

作者： Jbabdi, S. Woolrich, M. W. Andersson, J. L. R. Behrens, T. E. J. Univ Oxford John Radcliffe Hosp FMRIB Oxford OX3 9DU England Univ Oxford Dept Expt Psychol Oxford England

We readdress the diffusion tractography problem in a global and probabilistic manner. Instead of tracking through local orientations, we parameterise the connexions between brain regions at a global level, and then infer on global and local parameters simultaneously in a Bayesian framework. This approach offers a number of important benefits. The global nature of the tractography reduces sensitivity to local noise and modelling errors. By constraining tractography to ensure a connexion is found, and then inferring on the exact location of the connexion, we increase the robustness of connectivity-based parcellations, allowing parcellations of connexions that were previously invisible to tractography. The Bayesian framework allows a direct comparison of the evidence for connecting and non-connecting models, to test whether the connexion is supported by the data. Crucially, by explicit parameterisation of the connexion between brain regions, we infer on a parameter that is shared with models of functional connectivity. This model is a first step toward the joint inference on functional and anatomical connectivity. (c) 2007 Elsevier Inc. All rights reserved.

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Accurate cell segmentation in microscopy images using membrane patterns

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BIOINFORMATICS 2014年第18期30卷 2644-2651页

作者： Dimopoulos, Sotiris Mayer, Christian E. Rudolf, Fabian Stelling, Joerg ETH Dept Biosyst Sci & Engn CH-4058 Basel Switzerland ETH Swiss Inst Bioinformat CH-4058 Basel Switzerland

Motivation: Identifying cells in an image (cell segmentation) is essential for quantitative single-cell biology via optical microscopy. Although a plethora of segmentation methods exists, accurate segmentation is challenging and usually requires problem-specific tailoring of algorithms. In addition, most current segmentation algorithms rely on a few basic approaches that use the gradient field of the image to detect cell boundaries. However, many microscopy protocols can generate images with characteristic intensity profiles at the cell membrane. This has not yet been algorithmically exploited to establish more general segmentation methods. Results: We present an automatic cell segmentation method that decodes the information across the cell membrane and guarantees optimal detection of the cell boundaries on a per-cell basis. Graph cuts account for the information of the cell boundaries through directional cross-correlations, and they automatically incorporate spatial constraints. The method accurately segments images of various cell types grown in dense cultures that are acquired with different microscopy techniques. In quantitative benchmarks and comparisons with established methods on synthetic and real images, we demonstrate significantly improved segmentation performance despite cell-shape irregularity, cell-to-cell variability and image noise. As a proof of concept, we monitor the internalization of green fluorescent protein-tagged plasma membrane transporters in single yeast cells.

关键词： Algorithms Cell Membrane/metabolism Computational Biology/methods image processing, computer-assisted/methods Microscopy/methods

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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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Simultaneous intracellular recording and calcium imaging in single neurons of hippocampal slices

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methods-A COMPANION TO methods IN ENZYMOLOGY 2000年第4期21卷 373-383页

作者： Young, SR Wong, RKS Bianchi, R SUNY Hlth Sci Ctr Dept Physiol & Pharmacol Brooklyn NY 11203 USA

Fluorescent Ca2+ indicator dyes can be introduced into cells through the same microelectrode used for intracellular voltage recording. Simultaneous measurement of cell membrane potential and intracellular Ca2+ concentration can be very helpful in interpreting the mechanisms of Ca2+ increases. This chapter describes fluorescence image acquisition using a CCD camera and a computer program that also records a synchronized membrane potential trace. The same program allows for preliminary data analysis. More elaborate analyses can be accomplished with commercial programs. We also describe quantitative evaluations of sources of error in the use of the statistic Delta F/F as an indicator of Ca2+ concentration. Especially important errors to minimize are changes in background fluorescence and inappropriate autofluorescence corrections. Some improvement of fluorescence images of cells deep within slices may be accomplished by masking. One method is described for making a mash based on the raw fluorescence image. With another method, highly detailed cell morphologies may be conveyed by using masks based on neurobiotin injections and camera lucida drawings. (C) 2000 Academic Press.

关键词： Animals Calcium/metabolism Calcium Channels/physiology Fluorescent Dyes/pharmacology Hippocampus/cytology Hippocampus/physiology image processing, computer-assisted/methods Kinetics Microscopy, Video/instrumentation Microscopy, Video/methods Neurons/cytology Neurons/physiology Receptors, Glutamate/metabolism

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