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A reproducible evaluation of ANTs similarity metric performance in brain image registration

NEUROimage 2011年第3期54卷 2033-2044页

作者： Avants, Brian B. Tustison, Nicholas J. Song, Gang Cook, Philip A. Klein, Arno Gee, James C. Univ Penn Penn Image Comp & Sci Lab Philadelphia PA 19104 USA Columbia Univ New York State Psychiat Inst New York NY 10032 USA

The United States National Institutes of Health (NIH) commit significant support to open-source data and software resources in order to foment reproducibility in the biomedical imaging sciences. Here, we report and evaluate a recent product of this commitment: Advanced Neuroimaging Tools (ANTs), which is approaching its 2.0 release. The ANTs open source software library consists of a suite of state-of-the-art image registration, segmentation and template building tools for quantitative morphometric analysis. In this work, we use ANTs to quantify, for the first time, the impact of similarity metrics on the affine and deformable components of a template-based normalization study. We detail the ANTs implementation of three similarity metrics: squared intensity difference, a new and faster cross-correlation, and voxel-wise mutual information. We then use twofold cross-validation to compare their performance on openly available, manually labeled, T1-weighted MRI brain image data of 40 subjects (UCLA's LPBA40 dataset). We report evaluation results on cortical and whole brain labels for both the affine and deformable components of the registration. Results indicate that the best ANTs methods are competitive with existing brain extraction results (Jaccard = 0.958) and cortical labeling approaches. Mutual information affine mapping combined with cross-correlation diffeomorphic mapping gave the best cortical labeling results (Jaccard = 0.669 +/-0.022). Furthermore, our two-fold cross-validation allows us to quantify the similarity of templates derived from different subgroups. Our open code, data and evaluation scripts set performance benchmark parameters for this state-of-the-art toolkit This is the first study to use a consistent transformation framework to provide a reproducible evaluation of the isolated effect of the similarity metric on optimal template construction and brain labeling. (C) 2010 Elsevier Inc. All rights reserved.

关键词： Algorithms Brain/anatomy & histology Databases, Factual Diagnostic Imaging/methods Head/anatomy & histology Humans image processing, computer-assisted/methods Linear Models Models, Anatomic Models, Neurological Population Reproducibility of Results Software

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Tissue analysis by imaging MS

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BIOANALYSIS 2012年第1期4卷 95-112页

作者： Oppenheimer, Stacey R. Drexler, Dieter M. Pfizer Global Res & Dev World Wide Med Chem Groton CT 06340 USA Bristol Myers Squibb Co Res & Dev Discovery Analyt Sci Wallingford CT 06492 USA

Imaging MS (IMS) is generating tremendous interest in scientific communities because of its unparalleled capabilities to provide chemical analysis of intact tissue. Advances in analytical chemistry and MS are providing new insights into chemical and biological processes. This review will discuss various IMS platforms and their applications in biomedical and pharmaceutical research.

关键词： Animals Humans image processing, computer-assisted/methods Mass Spectrometry/methods Tissue Array Analysis/methods Tissue Distribution

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Automated image analysis of cytokinesis-blocked micronuclei: an adapted protocol and a validated scoring procedure for biomonitoring

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MUTAGENESIS 2009年第1期24卷 85-93页

作者： Decordier, Ilse Papine, Alexander Plas, Gina Roesems, Sam Vande Loock, Kim Moreno-Palomo, Jennifer Cemeli, Eduardo Anderson, Diana Fucic, Aleksandra Marcos, Ricardo Soussaline, Francoise Kirsch-Volders, Micheline Vrije Univ Brussel Lab Cellulaire Genet B-1050 Brussels Belgium IMSTAR F-75006 Paris France Univ Autonoma Barcelona Dept Genet & Microbiol Grp Mutagenesi Bellaterra Spain Univ Bradford Dept Biomed Sci Bradford BD7 1DP W Yorkshire England Inst Med Res & Occupat Hlth Zagreb 10000 Croatia

Micronuclei (MN) frequencies in peripheral blood lymphocytes have been used worldwide as a biomarker of chromosomal damage for genotoxicity testing and biomonitoring studies. Automation of MN analysis would provide faster and more reliable results with minimizing subjective MN identification. We developed an automated facility for the scoring of the in vitro MN cytokinesis-block assay for biomonitoring on Giemsa-stained slides, fulfilling the following criteria: applicable to the cytokinesis-block micronucleus methodology, discriminating between mono-, bi- and polynucleated cells, MN scoring according to HUMN scoring criteria, false-negative MN rate < 10% and false-positive (FP) MN rate < 1%. We first adapted the slide preparation protocol to obtain an optimal cell density and dispersion, which is important for image analysis. We developed specific algorithms starting from the cell as a detection unit. The whole detection and scoring process was separated into two distinct steps: in the first step, the cells and nuclei are detected;then, in the second step, the MN are searched for in the detected cells. Since the rate of FP MN obtained by the automatic analysis was in the range of 0.5-1.5%, an interactive visual validation step was introduced, which is not time consuming and allows quality control. Validation of the automated scoring procedure was undertaken by comparing the results of visual and automated scoring of micronucleated mono- and binucleated cells in human lymphocytes induced by two clastogens (ionizing radiation and methyl methane-sulphonate), two aneugens (nocodazole and carbendazim) and one apoptogen (staurosporine). Although the absolute MN frequencies obtained with automated scoring were lower as compared to those detected by visual scoring, a clear dose response for MNBN frequencies was observed with the automated scoring system, indicating that it is able to produce biologically relevant and reliable results. These observations, together with its

关键词： Adult Biological Markers Cytokinesis DNA Damage Environmental Monitoring/methods Humans image processing, computer-assisted/methods Lymphocytes/chemistry Lymphocytes/ultrastructure Micronuclei, Chromosome-Defective Micronucleus Tests Reproducibility of Results

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Detection of signal synchronizations in resting-state fMRI datasets

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NEUROimage 2006年第1期29卷 321-327页

作者： Thirion, B Dodel, S Poline, JB CEA DSV Dept Rech Med Serv Hosp Frederic Joliot F-91401 Orsay France

In this paper, we propose a generic framework for the analysis of steady-state fMRI datasets, applied here to resting-state datasets. Our approach avoids the introduction of user-defined seed regions for the study of spontaneous activity. Unlike existing techniques, it yields a sparse representation of resting-state activity networks which can be characterized and investigated fairly easily in a semi-interactive fashion. We proceed in several steps, based on the idea that spectral coherence of the fMRI time courses in the low frequency band carries the information of interest. In particular, we address the question of building adapted representations of the data from the spectral coherence matrix. We analyze nine datasets taken from three subjects and show resting-state networks validated by EEG-fMRI simultaneous acquisition literature, with low intra-subject variability;we also discuss the merits of different (rapid/slow) fMRI acquisition schemes. (c) 2005 Elsevier Inc. All rights reserved.

关键词： Algorithms Brain Mapping Brain Mapping Cluster Analysis computer Simulation Electroencephalography Humans image processing, computer-assisted/methods Magnetic Resonance Imaging/statistics & numerical data Multivariate Analysis Nerve Net/physiology

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ShapePheno: unsupervised extraction of shape phenotypes from biological image collections

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BIOINFORMATICS 2012年第7期28卷 1001-1008页

作者： Karaletsos, Theofanis Stegle, Oliver Dreyer, Christine Winn, John Borgwardt, Karsten M. Max Planck Inst Intelligent Syst Machine Learning & Computat Biol Res Grp D-72076 Tubingen Germany Max Planck Inst Dev Biol Dept Mol Biol D-72076 Tubingen Germany Microsoft Res Ltd Machine Learning & Percept Grp Cambridge CB3 0FB England Univ Tubingen Zentrum Bioinformat D-72076 Tubingen Germany

Motivation: Accurate large-scale phenotyping has recently gained considerable importance in biology. For example, in genomewide association studies technological advances have rendered genotyping cheap, leaving phenotype acquisition as the major bottleneck. Automatic image analysis is one major strategy to phenotype individuals in large numbers. Current approaches for visual phenotyping focus predominantly on summarizing statistics and geometric measures, such as height and width of an individual, or color histograms and patterns. However, more subtle, but biologically informative phenotypes, such as the local deformation of the shape of an individual with respect to the population mean cannot be automatically extracted and quantified by current techniques. Results: We propose a probabilistic machine learning model that allows for the extraction of deformation phenotypes from biological images, making them available as quantitative traits for downstream analysis. Our approach jointly models a collection of images using a learned common template that is mapped onto each image through a deformable smooth transformation. In a case study, we analyze the shape deformations of 388 guppy fish (Poecilia reticulata). We find that the flexible shape phenotypes our model extracts are complementary to basic geometric measures. Moreover, these quantitative traits assort the observations into distinct groups and can be mapped to polymorphic genetic loci of the sample set.

关键词： Animals Artificial Intelligence Cluster Analysis Computational Biology/methods image processing, computer-assisted/methods Male Markov Chains Models, Statistical Pattern Recognition, Automated/methods Phenotype Poecilia

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A method for generating reproducible evidence in fMRI studies

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NEUROimage 2006年第2期29卷 383-395页

作者： Liou, M Su, HR Lee, JD Aston, JAD Tsai, AC Cheng, PE Acad Sinica Inst Stat Sci Taipei 115 Taiwan

Insights into cognitive neuroscience from neuroimaging techniques are now required to go beyond the localisation of well-known cognitive functions. Fundamental to this is the notion of reproducibility of experimental outcomes. This paper addresses the central issue that functional magnetic resonance imaging (fMRI) experiments will produce more desirable information if researchers begin to search for reproducible evidence rather than only p value significance. The study proposes a methodology for investigating reproducible evidence without conducting separate fMRI experiments. The reproducible evidence is gathered from the separate runs within the study. The associated empirical Bayes and ROC extensions of the linear model provide parameter estimates to determine reproducibility. Empirical applications of the methodology suggest that reproducible evidence is robust to small sample sizes and sensitive to both the magnitude and persistency of brain activation. It is demonstrated that research findings in fMRI studies would be more compelling with supporting reproducible evidence in addition to standard hypothesis testing evidence. (c) 2005 Elsevier Inc. All rights reserved.

关键词： Algorithms Bayes Theorem Brain Mapping/methods Brain Mapping/methods Cerebral Cortex/physiology Data Interpretation, Statistical Humans image processing, computer-assisted/methods image processing, computer-assisted/statistics & numerical data Linear Models Magnetic Resonance Imaging/methods Magnetic Resonance Imaging/statistics & numerical data Reproducibility of Results ROC Curve Sample Size

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QUANTITATIVE ENDOSCOPY - PRECISE computerIZED MEASUREMENT OF METAPLASTIC EPITHELIAL SURFACE-AREA IN BARRETTS-ESOPHAGUS

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GASTROENTEROLOGY 1995年第2期108卷 360-366页

作者： KIM, R BAGGOTT, BB ROSE, S SHAR, AO MALLORY, DL LASKY, SS KRESSLOFF, M FACCENDA, LY REYNOLDS, JC UNIV PITTSBURGH DEPT MED PITTSBURGH PA USA UNIV PENN DEPT MED PHILADELPHIA PA USA UNIV PENN OFF INFORMAT TECHNOL PHILADELPHIA PA USA

Background/Aims: The inability to precisely measure the area of Barrett's metaplasia has impaired the study of its natural history and response to therapy. This study used a novel computer program that creates two-dimensional maps of the esophagus allowing for calculation of the area of Barrett's metaplasia. methods: Endoscopic photographs of Barrett's models and patients were obtained by independent endoscopists. The program transformed the photographs into maps, and the area of Barrett's metaplasia was calculated. Results: Using models, calculated areas correlated with actual areas (r = 0.96) with an overall error of 5.2%. Color, size, shape, diameter of the model, or endoscopist's experience did not affect the accuracy. Accuracy did improve by decreasing the interval between photographs from 4 cm (10.0% error) to 2 cm (4.8% error). In patients, area calculations from maps created by independent technicians correlated precisely (r = 0.99) at 1-cm (n = 22) and 2-cm (n = 40) intervals. Independent endoscopists correlated precisely in producing photographs for map construction (r = 0.99;n = 20). Conclusions: This novel computer technology produces two-dimensional maps of Barrett's metaplasia that can be used to accurately calculate area. Minimal interobserver variability in obtaining photographs is found.

关键词： Adult Barrett Esophagus/pathology Esophagoscopy Esophagoscopy Esophagus/pathology Humans image processing, computer-assisted/methods Metaplasia/pathology Observer Variation Reproducibility of Results

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Training Improves Multitasking Performance by Increasing the Speed of Information processing in Human Prefrontal Cortex

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NEURON 2009年第1期63卷 127-138页

作者： Dux, Paul E. Tombu, Michael N. Harrison, Stephenie Rogers, Baxter P. Tong, Frank Marois, Rene Vanderbilt Univ Dept Psychol Vanderbilt Vis Res Ctr Ctr Integrat & Cognit Neurosci Nashville TN 37240 USA Vanderbilt Univ Inst Imaging Sci Nashville TN 37240 USA Vanderbilt Univ Dept Radiol & Radiol Sci Nashville TN 37240 USA Univ Queensland Sch Psychol Brisbane Qld 4072 Australia

Our ability to multitask is severely limited: task performance deteriorates when we attempt to undertake two or more tasks simultaneously. Remarkably, extensive training can greatly reduce such multitasking costs. While it is not known how training alters the brain to solve the multitasking problem, it likely involves the prefrontal cortex given this brain region's purported role in limiting multitasking performance. Here, we show that the reduction of multitasking interference with training is not achieved by diverting the flow of information processing away from the prefrontal cortex or by segregating prefrontal cells into independent task-specific neuronal ensembles, but rather by increasing the speed of information processing in this brain region, thereby allowing multiple tasks to be processed in rapid succession. These results not only reveal how training leads to efficient multitasking, they also provide a mechanistic account of multitasking limitations, namely the poor speed of information processing in human prefrontal cortex.

关键词： Acoustic Stimulation Adult Brain Mapping Brain Mapping Female Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Male Mental Processes/physiology Oxygen/blood Photic Stimulation/methods Prefrontal Cortex/blood supply Prefrontal Cortex/physiology Psychomotor Performance/physiology Reaction Time/physiology Task Performance and Analysis Teaching/methods Young Adult

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SEMIAUTOMATIC QUANTITATION OF DENSE MARKERS IN CYTOCHEMISTRY

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HISTOCHEMISTRY 1991年第3期96卷 245-250页

作者： LEBONVALLET, S MENNESSON, T BONNET, N GIROD, S PLOTKOWSKI, C HINNRASKY, J PUCHELLE, E 1. Unité INSERM 314 Université de Reims 21 Rue Clément Ader F-51100 Reims France

The quantitation of electron dense labelling is very tedious when it is done "by hand". Accordingly we developed software allowing, at electron microscopic level, a semi-automatic counting of dense markers in biological specimens. It includes the digitization of images and extraction of dense particles from the grey level of the background. The definition of the areas of interest was carried out by the observer but all quantitative calculations were done automatically. This method was applied to different biological materials (phospholipid and lysozyme labelling in secretory granules of human submucosal bronchial gland cells). The results obtained by this semi-automatic procedure were in good agreement with those obtained by manual counting of colloidal gold labelling (r = 0.97).

关键词： Automation Histocytochemistry/methods Histocytochemistry/methods image processing, computer-assisted/methods Microscopy, Immunoelectron Software Staining and Labeling Staining and Labeling

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A High-Resolution Imaging Approach to Investigate Chromatin Architecture in Complex Tissues

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CELL 2015年第1期163卷 246-255页

作者： Linhoff, Michael W. Garg, Saurabh K. Mandel, Gail Oregon Hlth & Sci Univ Vollum Inst Portland OR 97239 USA Oregon Hlth & Sci Univ Howard Hughes Med Inst Portland OR 97239 USA

We present ChromATin, a quantitative high-resolution imaging approach for investigating chromatin organization in complex tissues. This method combines analysis of epigenetic modifications by immunostaining, localization of specific DNA sequences by FISH, and high-resolution segregation of nuclear compartments using array tomography (AT) imaging. We then apply this approach to examine how the genome is organized in the mammalian brain using female Rett syndrome mice, which are a mosaic of normal and Mecp2-null cells. Side-by-side comparisons within the same field reveal distinct heterochromatin territories in wild-type neurons that are altered in Mecp2-null nuclei. Mutant neurons exhibit increased chromatin compaction and a striking redistribution of the H4K20me3 histone modification into pericentromeric heterochromatin, a territory occupied normally by MeCP2. These events are not observed in every neuronal cell type, highlighting ChromATin as a powerful in situ method for examining cell-type-specific differences in chromatin architecture in complex tissues.

关键词： Animals Brain/metabolism Cell Nucleus/metabolism Chromatin/metabolism Female Heterochromatin/metabolism Histones/metabolism image processing, computer-assisted/methods In Situ Hybridization, Fluorescence In Situ Hybridization, Fluorescence Methyl-CpG-Binding Protein 2/genetics Methyl-CpG-Binding Protein 2/metabolism Mice Neurons/metabolism Rett Syndrome/genetics Rett Syndrome/metabolism Tomography/methods

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