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PATHOLOGY 2010年第3期42卷 205-206页

作者： Leong, Anthony S-Y. John Hunter Hosp Hunter Area Pathol Serv Newcastle NSW Australia

The article presents the author's views on objectivity in digital image analysis performed by computers for medical purposes. According to the author, diagnosis formulation is a knowledge-based process, and is applied in combination with visual recognition. The author says that the diagnostic process is very complicated, which is based on the experience of the pathologist, and the clinical circumstances of the patient.

关键词： Humans image processing, computer-assisted/methods image processing, computer-assisted/standards

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Waxholm Space: An image-based reference for coordinating mouse brain research

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NEUROimage 2010年第2期53卷 365-372页

作者： Johnson, G. Allan Badea, Alexandra Brandenburg, Jeffrey Cofer, Gary Fubara, Boma Liu, Song Nissanov, Jonathan Duke Univ Med Ctr Ctr Vivo Microscopy Durham NC 27710 USA Drexel Univ Coll Med Dept Neurobiol & Anat Philadelphia PA 19129 USA Touro Univ Nevada Dept Basic Sci Henderson NV 89014 USA

We describe an atlas of the C57BL/6 mouse brain based on MRI and conventional Nissl histology Magnetic resonance microscopy was performed on a total of 14 specimens that were actively stained to enhance tissue contrast. images were acquired with three different MR protocols yielding contrast dependent on spin lattice relaxation (T1), spin spin relaxation (T2). and magnetic susceptibility (T2*). Spatial resolution was 21 5 mu m (isotropic) Conventional histology (Nissl) was performed on a limited set of these same specimens and the Nissl images were registered (3D-to-3D) to the MR data Probabilistic atlases for 37 structures are provided. along with average atlases. The availability of three different MR protocols, the Nissl data, and the labels provides a rich set of options for registration of other atlases to the same coordinate system, thus facilitating data-sharing All the data is available for download via the web (C) 2010 Elsevier Inc. All rights reserved

关键词： Animals Atlases as Topic Brain/anatomy & histology Databases, Factual Histology image processing, computer-assisted/standards Imaging, Three-Dimensional/methods Magnetic Resonance Imaging Male Mice/anatomy & histology Mice, Inbred C57BL Reference standards Staining and Labeling Staining and Labeling Thalamus/anatomy & histology

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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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Template-O-Matic: A toolbox for creating customized pediatric templates

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NEUROimage 2008年第3期41卷 903-913页

作者： Wilke, Marko Holland, Scott K. Altaye, Mekibib Gaser, Christian Univ Tubingen Childrens Hosp Dept Pediat Neurol & Dev Med D-72076 Tubingen Germany Univ Tubingen Dept Neuroradiol CNS Sect Expt MR Tubingen Germany Childrens Hosp Med Ctr Imaging Res Ctr Cincinnati OH 45229 USA Univ Cincinnati Dept Pediat Cincinnati OH 45221 USA Univ Jena Dept Psychiat D-6900 Jena Germany

processing pediatric neuroimaging data is a challenge due to pervasive morphological changes that occur in the human brain during normal development. This is of special relevance when reference data is used as part of the processing approach, as in spatial normalization and tissue segmentation. Current approaches construct reference data (templates) by averaging brain images from a control group of subjects, or by creating custom templates from the group under study. In this technical note, we describe a new, and generalized method of constructing such appropriate reference data by statistically analyzing a large sample (n= 404) of healthy children, as acquired during the NIH MRI study of normal brain development. After eliminating non-contributing demographic variables, we modeled the effects of age (first, second, and third-order terms) and gender, for each voxel in gray matter and white matter. By appropriate weighting with the parameter estimates from these analyses, complete tissue maps can be generated automatically from this database to match a pediatric population selected for study. The algorithm is implemented in the form of a toolbox for the SPM5 image data processing suite, which we term Template-O-Matic. We compare the performance of this approach with the current method of template generation and discuss the implications of our approach. (C) 2008 Elsevier Inc. All rights reserved.

关键词： Adolescent Algorithms Brain/anatomy & histology Child Humans image processing, computer-assisted/methods image processing, computer-assisted/standards Magnetic Resonance Imaging Reference standards

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Accuracy of helical computed tomographic angiography for the diagnosis of colonic angiodysplasia

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GASTROENTEROLOGY 2000年第2期119卷 293-299页

作者： Junquera, F Quiroga, S Saperas, E Pérez-Lafuente, M Videla, S Alvarez-Castells, A Miró, JRA Malagelada, JR Autonomous Univ Barcelona Digest Syst Res Unit Hosp Gen Vall dHebron E-08035 Barcelona Spain Autonomous Univ Barcelona Dept Radiol Hosp Gen Vall dHebron E-08035 Barcelona Spain

Background & Aims: The diagnosis of colonic angiodysplasia is often challenging and relies on endoscopy or catheter angiography. We investigated whether computed tomographic angiography (CTA) contributes to the diagnosis of colonic angiodysplasia. Methods: Twenty-eight patients with suspected bleeding from colonic angiodysplasia were prospectively evaluated. Gastrointestinal bleeding was investigated by colonoscopy plus visceral angiography and by CTA. The level of agreement between CTA and the former procedures was determined. Results: CTA images of diagnostic quality were obtained in 26 patients. Eighteen patients were diagnosed with colonic angiodysplasia by colonoscopy plus visceral angiography, and 14 by CTA (kappa = 0.68;P < 0.001). Sensitivity, specificity, and positive predictive values of CTA for detection of colonic angiodysplasia were 70%, 100%, and 100%, respectively. CTA signs including accumulation of vessels in the colonic wall, early filling vein, and supplying enlarged artery were present in 55%, 50%, and 22% of cases, respectively. None of these signs were present in the 8 patients with obscure gastrointestinal bleeding and negative diagnostic investigation of the digestive tract. Conclusions: CTA is a sensitive, specific, well-tolerated, and minimally invasive tool for the diagnosis of colonic angiodysplasia.

关键词： Aged Aged, 80 and over Angiodysplasia/radiography Angiography/methods Angiography/standards Colon/blood supply Colonic Diseases/radiography Female Gastrointestinal Hemorrhage/radiography Humans image processing, computer-assisted/methods image processing, computer-assisted/standards Male Middle Aged Prospective Studies Reproducibility of Results Tomography, X-Ray Computed/standards

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Using collective expert judgements to evaluate quality measures of mass spectrometry images

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BIOINFORMATICS 2015年第12期31卷 375-384页

作者： Palmer, Andrew Ovchinnikova, Ekaterina Thune, Mikael Lavigne, Regis Guevel, Blandine Dyatlov, Andrey Vitek, Olga Pineau, Charles Boren, Mats Alexandrov, Theodore European Mol Biol Lab Heidelberg Germany Univ Bremen Ctr Ind Math D-28359 Bremen Germany Karlsruhe Inst Technol Inst Anthropomat High Performance Humanoid Technol Lab D-76021 Karlsruhe Germany Denator Uppsala Sweden Univ Rennes 1 Protim Inserm Irset U1085 Rennes France SCiLS GmbH Bremen Germany Northeastern Univ Coll Comp & Informat Sci Boston MA 02115 USA Univ Calif San Diego Skaggs Sch Pharm & Pharmaceut Sci La Jolla CA 92093 USA

Motivation: Imaging mass spectrometry (IMS) is a maturating technique of molecular imaging. Confidence in the reproducible quality of IMS data is essential for its integration into routine use. However, the predominant method for assessing quality is visual examination, a time consuming, unstandardized and non-scalable approach. So far, the problem of assessing the quality has only been marginally addressed and existing measures do not account for the spatial information of IMS data. Importantly, no approach exists for unbiased evaluation of potential quality measures. Results: We propose a novel approach for evaluating potential measures by creating a gold-standard set using collective expert judgements upon which we evaluated image-based measures. To produce a gold standard, we engaged 80 IMS experts, each to rate the relative quality between 52 pairs of ion images from MALDI-TOF IMS datasets of rat brain coronal sections. Experts' optional feedback on their expertise, the task and the survey showed that (i) they had diverse backgrounds and sufficient expertise, (ii) the task was properly understood, and (iii) the survey was comprehensible. A moderate inter-rater agreement was achieved with Krippendorff's alpha of 0.5. A gold-standard set of 634 pairs of images with accompanying ratings was constructed and showed a high agreement of 0.85. Eight families of potential measures with a range of parameters and statistical descriptors, giving 143 in total, were evaluated. Both signal-to-noise and spatial chaos-based measures performed highly with a correlation of 0.7 to 0.9 with the gold standard ratings. Moreover, we showed that a composite measure with the linear coefficients (trained on the gold standard with regularized least squares optimization and lasso) showed a strong linear correlation of 0.94 and an accuracy of 0.98 in predicting which image in a pair was of higher quality.

关键词： Animals Brain/anatomy & histology Brain/cytology Humans image processing, computer-assisted/standards Mice Molecular Imaging/methods Observer Variation Pilot Projects Quality Control Rats Reference standards Spectrometry, Mass, Matrix-assisted Laser Desorption-Ionization/methods

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Phase based venous suppression in resting-state BOLD GE-fMRI

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NEUROimage 2014年 100卷 51-59页

作者： Curtis, Andrew T. Hutchison, R. Matthew Menon, Ravi S. Univ Western Ontario Robarts Res Inst Ctr Funct & Metab Mapping London ON N6A 5K8 Canada Univ Western Ontario Dept Med Biophys London ON N6A 5C1 Canada Harvard Univ Ctr Brain Sci Cambridge MA 02138 USA

Resting-state functional MRI (RS-fMRI) is a widely used method for inferring connectivity between brain regions or nodes. As with task-based fMRI, the spatial specificity of the connectivity maps can be distorted by the strong biasing effect of the BOLD signal in macroscopic veins. In RS-fMRI this effect is exacerbated by the temporal coherences of physiological origin between large veins that are widely distributed in the brain. In gradient echo based EPI, used for the vast majority of RS-fMRI, macroscopic veins that carry BOLD-related changes exhibit a strong phase response. This allows for post-processing identification and removal of venous signals using a phase regressor technique. Here, we employ this approach to suppress macrovascular venous contributions in high-field whole-brain RS-fMRI data sets, resulting in significant changes to both the spatial localization of the networks and the correlations between the network nodes. These effects were observed at both the individual and group analysis level, suggesting that venous contamination is a confounding factor for RS-fMRI studies even at relatively low image resolutions. Suppression of the macrovascular signal using the phase regression approach may therefore help to better identify, delineate, and interpret the true structure of large-scale brain networks. (C) 2014 Elsevier Inc. All rights reserved.

关键词： Adult Brain/blood supply Brain/physiology Brain Mapping/methods Brain Mapping/methods Brain Mapping/standards Brain Mapping/standards Cerebral Veins/anatomy & histology Female Humans image processing, computer-assisted/methods image processing, computer-assisted/standards Magnetic Resonance Imaging Male Young Adult

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Robust variables in texture analysis

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PATHOLOGY 2010年第6期42卷 609-610页

作者： Metze, Konradin Adam, Randall L. Ferreira, Rita C. Univ Estadual Campinas Fac Med Dept Pathol Campinas SP Brazil Univ Estadual Campinas Inst Comp Campinas SP Brazil

A letter to the editor is presented in response to the article "On the concept of objectivity in digital image analysis in pathology," by P. J. Tadrous in the 2010 issue.

关键词： Humans image processing, computer-assisted/standards Staining and Labeling/standards Staining and Labeling/standards

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Digital Imaging and Communications in Medicine (DICOM) as standard in digital pathology

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HISTOPATHOLOGY 2012年第1期61卷 132-134页

作者： Kalinski, Thomas Zwoenitzer, Ralf Rossner, Mathias Hofmann, Harald Roessner, Albert Guenther, Thomas Otto Von Guericke Univ Dept Pathol Magdeburg Germany Imassense Deutschland GmbH Berlin Germany Univ Hosp Dept Pathol & Neuropathol Essen Germany Otto Von Guericke Univ Dept Med IT Magdeburg Germany St Marks Hosp Acad Dept Histopathol Harrow Middx England

A letter to the editor is presented in response to a review by Al-Janabi and colleagues on the use of digital imaging systems in histopathology.

关键词： Diagnostic Imaging/methods Diagnostic Imaging/standards Humans image processing, computer-assisted/methods image processing, computer-assisted/standards Imaging, Three-Dimensional/instrumentation Imaging, Three-Dimensional/standards Pathology, Surgical/methods Signal processing, computer-assisted/instrumentation Telepathology/instrumentation Telepathology/methods

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Seeing clearly is not necessarily believing

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NATURE 2005年第7039期435卷 143-143页

作者： Greene, MT Univ Puget Sound Honors Program Tacoma WA 98416 USA

Presents a letter to the editor in response to the article "CSI: Cell Biology," published in previous issue.

关键词： Clathrin/ultrastructure Cryoelectron Microscopy/methods Cryoelectron Microscopy/standards Disclosure/standards Disclosure/standards image processing, computer-assisted/ethics image processing, computer-assisted/methods image processing, computer-assisted/standards Research/methods Research/standards Software

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