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Optimization of large-scale mouse brain connectome via joint evaluation of DTI and neuron tracing data

NEUROimage 2015年 115卷 202-213页

作者： Chen, Hanbo Liu, Tao Zhao, Yu Zhang, Tuo Li, Yujie Li, Meng Zhang, Hongmiao Kuang, Hui Guo, Lei Tsien, Joe Z. Liu, Tianming Univ Georgia Cort Architecture Imaging & Discovery Lab Dept Comp Sci Athens GA 30602 USA Univ Georgia Bioimaging Res Ctr Athens GA 30602 USA Hebei United Univ Tangshan Hebei Peoples R China Northwestern Polytech Univ Sch Automat Xian 710072 Peoples R China GA Regents Univ Brain & Behav Discovery Inst Med Coll Georgia Augusta GA 30912 USA

Tractography based on diffusion tensor imaging (DTI) data has been used as a tool by a large number of recent studies to investigate structural connectome. Despite its great success in offering unique 3D neuroanatomy information, DTI is an indirect observation with limited resolution and accuracy and its reliability is still unclear. Thus, it is essential to answer this fundamental question: how reliable is DTI tractography in constructing large-scale connectome? To answer this question, we employed neuron tracing data of 1772 experiments on the mouse brain released by the Allen Mouse Brain Connectivity Atlas (AMCA) as the ground-truth to assess the performance of DTI tractography in inferring white matter fiber pathways and inter-regional connections. For the first time in the neuroimaging field, the performance of whole brain DTI tractography in constructing a large-scale connectome has been evaluated by comparison with tracing data. Our results suggested that only with the optimized tractography parameters and the appropriate scale of brain parcellation scheme, can DTI produce relatively reliable fiber pathways and a large-scale connectome. Meanwhile, a considerable amount of errors were also identified in optimized DTI tractography results, which we believe could be potentially alleviated by efforts in developing better DTI tractography approaches. In this scenario, our framework could serve as a reliable and quantitative test bed to identify errors in tractography results which will facilitate the development of such novel tractography algorithms and the selection of optimal parameters. (C) 2015 Elsevier Inc. All rights reserved.

关键词： Algorithms Animals Atlases as Topic Brain/anatomy & histology Brain Mapping Brain Mapping Connectome Diffusion Tensor Imaging/methods Diffusion Tensor Imaging/methods Functional Laterality/physiology image processing, computer-assisted/methods Imaging, Three-Dimensional Mice/anatomy & histology Nerve Fibers Neural Pathways/anatomy & histology Neurons/physiology Reproducibility of Results

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Structured sparsity for spatially coherent fibre orientation estimation in diffusion MRI

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NEUROimage 2015年 115卷 245-255页

作者： Auria, A. Daducci, A. Thiran, J. -P. Wiaux, Y. Ecole Polytech Fed Lausanne Signal Proc Lab LTS5 CH-1015 Lausanne Switzerland Univ Hosp Ctr CHUV Lausanne Switzerland Univ Lausanne UNIL CH-1015 Lausanne Switzerland Heriot Watt Univ Inst Sensors Signals & Syst Edinburgh Midlothian Scotland

We propose a novel formulation to solve the problem of intra-voxel reconstruction of the fibre orientation distribution function (FOD) in each voxel of the white matter of the brain from diffusion MRI data. The majority of the state-of-the-art methods in the field perform the reconstruction on a voxel-by-voxel level, promoting sparsity of the orientation distribution. Recent methods have proposed a global denoising of the diffusion data using spatial information prior to reconstruction, while others promote spatial regularisation through an additional empirical prior on the diffusion image at each q-space point. Our approach reconciles voxelwise sparsity and spatial regularisation and defines a spatially structured FOD sparsity prior, where the structure originates from the spatial coherence of the fibre orientation between neighbour voxels. The method is shown, through both simulated and real data, to enable accurate FOD reconstruction from a much lower number of q-space samples than the state of the art, typically 15 samples, even for quite adverse noise conditions. (C) 2015 Elsevier Inc. All rights reserved.

关键词： Algorithms computer Simulation Databases, Factual Diffusion Magnetic Resonance Imaging/methods Humans image processing, computer-assisted/methods Nerve Fibers/physiology Phantoms, Imaging White Matter/anatomy & histology White Matter/cytology

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SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function

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CELL 2015年第7期163卷 1796-1806页

作者： Tomer, Raju Lovett-Barron, Matthew Kauvar, Isaac Andalman, Aaron Burns, Vanessa M. Sankaran, Sethuraman Grosenick, Logan Broxton, Michael Yang, Samuel Deisseroth, Karl Stanford Univ Dept Bioengn Stanford CA 94305 USA Stanford Univ CNC Program Stanford CA 94305 USA Stanford Univ Dept Elect Engn Stanford CA 94305 USA Stanford Univ Dept Chem & Syst Biol Stanford CA 94305 USA Stanford Univ Dept Comp Sci Stanford CA 94305 USA Stanford Univ Howard Hughes Med Inst Stanford CA 94305 USA Stanford Univ Dept Psychiat & Behav Sci Stanford CA 94305 USA

The goal of understanding living nervous systems has driven interest in high-speed and large field-of-view volumetric imaging at cellular resolution. Light sheet microscopy approaches have emerged for cellular-resolution functional brain imaging in small organisms such as larval zebrafish, but remain fundamentally limited in speed. Here, we have developed SPED light sheet microscopy, which combines large volumetric field-of-view via an extended depth of field with the optical sectioning of light sheet microscopy, thereby eliminating the need to physically scan detection objectives for volumetric imaging. SPED enables scanning of thousands of volumes-per-second, limited only by camera acquisition rate, through the harnessing of optical mechanisms that normally result in unwanted spherical aberrations. We demonstrate capabilities of SPED microscopy by performing fast sub-cellular resolution imaging of CLARITY mouse brains and cellular-resolution volumetric Ca2+ imaging of entire zebrafish nervous systems. Together, SPED light sheet methods enable high-speed cellular-resolution volumetric mapping of biological system structure and function.

关键词： Animals Brain/cytology image processing, computer-assisted/methods Larva/cytology Mice Microscopy/methods Nervous System/cytology Neurites/ultrastructure Zebrafish/growth & development

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A NOVEL PRINCIPLE FOR QUANTITATION OF FAST INTRACELLULAR CALCIUM CHANGES USING FURA-2 AND A MODIFIED image-processing SYSTEM - APPLICATIONS IN STUDIES OF NEUTROPHIL MOTILITY AND PHAGOCYTOSIS

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CELL CALCIUM 1992年第8期13卷 473-486页

作者： GUSTAFSON, M MAGNUSSON, KE Department of Medical Microbiology Faculty of Health Sciences University of Linköping Sweden.

A new principle is described for imaging intracellular free calcium [Ca2+]i changes in single, living cells utilizing the fluorescent probe Fura-2. It is based upon video color mixing in real time and allows high-speed visualization, at maximum image resolution, of [Ca2+]i changes without digital image ratioing. The epifluorescence images produced by 340 and 380 nm excitations are stored in two memory buffers of a personal computer-based image processing system. Two video signals are generated independently from each buffer and connected to the red and green inputs of a video display. An image is this way created, in which [Ca2+]i shows up as a specific hue, whereas changes in dye concentration, light intensity, cell thickness show up as variations in brightness of the imaged cells. The method has advantages over conventional ratio imaging, notably simplicity and speed, since no calculations are made. Yet it can be combined with traditional digital image processing. The imaging technique allows monitoring of [Ca2+]i changes in rapidly moving cells, like neutrophils. It is demonstrated that during random locomotion on serum-coated glass surfaces, [Ca2+]i levels appeared to oscillate and that the frequency of the oscillations are related to locomotive activity. Furthermore, in Ca2+ free medium, the cells continue to move and phagocytose in the presence of Ca2+ ionophore (ionomycin) and 2 mM EGTA. In the presence of 1 mM extracellular Ca2+, ionomycin-treated cells were not able to move or phagocytose.

关键词： Calcium/metabolism Calibration Cell Movement/physiology Color Egtazic Acid/pharmacology Egtazic Acid/pharmacology Fluorescence Fluorescence Fura-2 Histocytochemistry/methods Histocytochemistry/methods Humans image processing, computer-assisted/methods Neutrophils/metabolism Phagocytosis/physiology Phagocytosis/physiology Video Recording

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Measurement of optic disc compliance by digitized image analysis in the normal monkey eye

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OPHTHALMOLOGY 1995年第12期102卷 1790-1799页

作者： Burgoyne, CF Quigley, HA Thompson, HW Vitale, S Varma, R JOHNS HOPKINS SCH MED WILMER INSTGLAUCOMA SERVBALTIMOREMD JOHNS HOPKINS SCH MED WILMER INSTDANA CTR PREVENT OPHTHALMOLBALTIMOREMD UNIV SO CALIF SCH MEDDOHENY EYE INSTLOS ANGELESCA

Purpose: To characterize the compliance of the normal monkey optic disc under conditions of induced short-term fluctuations in intraocular pressure (IOP). methods: In 10 monkeys, one eye was compliance tested on three separate days followed by a single test of the contralateral eye (40 compliance tests). In a testing session, the optic disc was imaged at 2 and 47 minutes (baseline time point) after IOP was lowered to 10 mmHg;then at 2, 17, 32, and 47 minutes after IOP was elevated to 45 mmHg;then at 2, 47, and, in some cases, 92 minutes after IOP was lowered back to 10 mmHg. Eight digitized images were analyzed at each time point, yielding two parameters to characterize the position of the disc: the Mean Position of the Disc (MPD) and the Change from MPD(Baseline) (the value of MPD at a given time point minus the value for MPD at the baseline time point of that testing session). Analysis of variance (ANOVA) testing was used to evaluate the overall effect of IOF on both parameters while taking into account the effects of variability due to different monkeys and repetitions of the test as well as differences between the two eyes of an individual monkey. With the addition of data from 11 compliance tests performed on eight additional monkeys, the overall results were calculated in terms of the mean Change from MPD(Baseline) at each time point for a total of 51 compliance testing sessions. Results: The mean Change from MPD(Baseline) was -28 mu m (95% confidence interval, -23 to -33 mu m) 47 minutes after elevation of IOP. The disc surface returned to its baseline position 92 minutes after IOP was lowered back to 10 mmHg. Elevation of IOP within a compliance test had a significant effect on the position of the optic disc surface (P = 0.0002, ANOVA), as characterized by the parameter Change from MPD(Baseline) Neither the difference in the amount of movement between the two eyes of an individual monkey nor the variability within the three repetitions of the test in a given

关键词： Analysis of Variance Animals Elastic Tissue Elasticity image processing, computer-assisted/methods Intraocular Pressure Macaca fascicularis Male Ocular Hypertension/physiopathology Ocular Hypotension/physiopathology Optic Disk/pathology Optic Disk/physiopathology Reproducibility of Results

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Fibertract segmentation in position orientation space from high angular resolution diffusion MRI

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NEUROimage 2006年第2期32卷 665-675页

作者： Hagmann, Patric Jonasson, Lisa Deffieux, Thomas Meuli, Reto Thiran, Jean-Philippe Wedeen, Van J. Univ Lausanne Hosp CHU Vaudois Dept Radiol CH-1011 Lausanne Switzerland Ecole Polytech Fed Lausanne Signal Proc Inst Lausanne Switzerland Harvard Univ Sch Med Dept Radiol MGH Martinos Ctr Biomed Imaging Charlestown MA 02129 USA

In diffusion MRI, standard approaches for fibertract identification are based on algorithms that generate lines of coherent diffusion, currently known as tractography. A tract is then identified as a set of such lines selected on some criteria. In the present study, we investigate whether fibertract identification can be formulated as a segmentation task that recognizes a fibertract as a region where diffusion is intense and coherent. Indeed, we show that it is possible to segment efficiently well-known fibertracts with classical image processing methods provided that the problem is formulated in a five-dimensional space of position and orientation. As an example, we choose to adapt to this newly defined high-dimensional non-Euclidean space, called position orientation space, an algorithm based on the hidden Markov random field framework. Structures such as the cerebellar peduncles, corticospinal tract, association bundles can be identified and represented in three dimensions by a back projection technique similar to maximum intensity projection. Potential advantages and drawbacks as compared to classical tractography are discussed;for example, it appears that our formulation handles naturally crossing tracts and is not biased by human intervention. (c) 2006 Elsevier Inc. All rights reserved.

关键词： Algorithms Brain/anatomy & histology Brain Mapping Brain Mapping Brain Stem/anatomy & histology Diffusion Magnetic Resonance Imaging/methods Dominance, Cerebral/physiology Fourier Analysis Fourier Analysis Humans image processing, computer-assisted/methods Imaging, Three-Dimensional/methods Markov Chains Mathematical Computing Nerve Fibers/ultrasonography Neural Pathways/anatomy & histology Software

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The Chronnectome: Time-Varying Connectivity Networks as the Next Frontier in fMRI Data Discovery

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NEURON 2014年第2期84卷 262-274页

作者： Calhoun, Vince D. Miller, Robyn Pearlson, Godfrey Adali, Tulay Mind Res Network Albuquerque NM 87106 USA LBERI Albuquerque NM 87106 USA Univ New Mexico Dept ECE Albuquerque NM 87131 USA Univ Maryland Baltimore Cty Dept CSEE Baltimore MD 21250 USA Olin Neuropsychiat Res Ctr Hartford CT 06114 USA

Recent years have witnessed a rapid growth of interest in moving functional magnetic resonance imaging (fMRI) beyond simple scan-length averages and into approaches that capture time-varying properties of connectivity. In this Perspective we use the term "chronnectome" to describe metrics that allow a dynamic view of coupling. In the chronnectome, coupling refers to possibly time-varying levels of correlated or mutually informed activity between brain regions whose spatial properties may also be temporally evolving. We primarily focus on multivariate approaches developed in our group and review a number of approaches with an emphasis on matrix decompositions such as principle component analysis and independent component analysis. We also discuss the potential these approaches offer to improve characterization and understanding of brain function. There are a number of methodological directions that need to be developed further, but chronnectome approaches already show great promise for the study of both the healthy and the diseased brain.

关键词： Animals Brain/physiology Brain Mapping/methods Brain Mapping/methods Humans image processing, computer-assisted/methods Magnetic Resonance Imaging/methods Neural Pathways/physiology Time Factors

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Automatic denoising of functional MM data: Combining independent component analysis and hierarchical fusion of classifiers

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NEUROimage 2014年 90卷 449-468页

作者： Salimi-Khorshidi, Gholamreza Douaud, Gwenaelle Beckmann, Christian F. Glasser, Matthew F. Griffanti, Ludovica Smith, Stephen M. Univ Oxford Ctr Funct MRI Brain FMRIB Oxford England Radboud Univ Nijmegen Donders Inst Brain Cognit & Behav NL-6525 ED Nijmegen Netherlands Univ Twente MIRA Inst Biomed Technol & Tech Med NL-7500 AE Enschede Netherlands Washington Univ Sch Med St Louis MO USA Politecn Milan Dept Elect Informat & Bioengn I-20133 Milan Italy Fdn Don Carlo Gnocchi ONLUS MR Lab Milan Italy

Many sources of fluctuation contribute to the fMRI signal, and this makes identifying the effects that are truly related to the underlying neuronal activity difficult. Independent component analysis (ICA) - one of the most widely used techniques for the exploratory analysis of fMRI data - has shown to be a powerful technique in identifying various sources of neuronally-related and artefactual fluctuation in fIVIRI data (both with the application of external stimuli and with the subject "at rest"). ICA decomposes fMRI data into patterns of activity (a set of spatial maps and their corresponding time series) that are statistically independent and add linearly to explain voxelwise time series. Given the set of ICA components, if the components representing "signal" (brain activity) can be distinguished form the "noise" components (effects of motion, non-neuronal physiology, scanner artefacts and other nuisance sources), the latter can then be removed from the data, providing an effective cleanup of structured noise. Manual classification of components is labour intensive and requires expertise;hence, a fully automatic noise detection algorithm that can reliably detect various types of noise sources (in both task and resting fMRI) is desirable. In this paper, we introduce FIX ("FMRIB's ICA-based X-noiseifier"), which provides an automatic solution for denoising fMRI data via accurate classification of ICA components. For each ICA component FIX generates a large number of distinct spatial and temporal features, each describing a different aspect of the data (e.g., what proportion of temporal fluctuations are at high frequencies). The set of features is then fed into a multi-level classifier (built around several different classifiers). Once trained through the handclassification of a sufficient number of training datasets, the classifier can then automatically classify new datasets. The noise components can then be subtracted from (or regressed out of) the original data,

关键词： Algorithms Artifacts Brain/physiology Brain Mapping/methods Brain Mapping/methods Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Principal Component Analysis

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ESTIMATING INTRACELLULAR PH IN DEVELOPING RODENT EMBRYOS USING A computer IMAGING TECHNIQUE - CHANGES IN EMBRYONIC PH AND PROLIFERATION RATES FOLLOWING MATERNAL TREATMENT WITH ACETAZOLAMIDE

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TERATOLOGY 1995年第3期52卷 160-168页

作者： SCHREINER, CM COLLINS, MD SCOTT, WJ VORHEES, CV COLVIN, J MCCANDLESS, D CHILDRENS HOSP RES FDN DEPT PEDIATCINCINNATIOH 45229 CHICAGO MED SCH DEPT CELL BIOL & ANATN CHICAGOIL 60064

Using the transplacental distribution of the weak acid 5,5-dimethyloxazolidine-2,4-dione (DMO), a computer assisted imaging technique has been developed to permit the estimation of intracellular pH (pH(i)) in very specific areas of the developing rodent embryo. The study reported here demonstrates the heterogeneity of radiolabeled DMO distribution in the developing mouse forelimb. The pattern of pH(i) distribution shifts from one of high pH(i) values in the proximal core of the mesoderm on day 10 of gestation to one of higher pH(i) values in the mesoderm lust underlying the ectoderm on day 11. Studies [Scott et al. (1990) Toxicol. Appl. Pharmacol. 103:238-254] in which DMO concentration was monitored following treatment with acetazolamide or acetazolamide plus amiloride were done in whole embryo homogenates or pooled limb samples which allow for the calculation of an average pH(i) but may not reflect the pH(i) in very specific locations of the limb. Two hours after acetazolamide administration, the pH(i) pattern was not significantly changed from control. Intracellular pH was raised above control levels but was not significant statistically except in the peripheral mesoderm in the ventral third of the forelimb. Fifteen hours after acetazolamide treatment, there was a significant decrease in pH(i) values with no change in pattern. However, treatment with acetazolamide plus amiloride for 15 hr produced a marked reduction of pH(i) values throughout the forelimb bud. Changes in bromodeoxyuridine labeling index lan indication of proliferative activity following treatment with acetazolamide or acetazolamide plus amiloride are reported. The combination treatment reduced the labeling index by approximately 15% below that of control embryos in the limb region where absence of digit(s) will occur. However, we found no overall correlation of proliferative rate and pH(i) of limb bud mesoderm in treated embryos. Consequently, we were unable to causally associate reduced pH(i) wi

关键词： Abnormalities, Drug-Induced/metabolism Acetazolamide Amiloride/toxicity Animals Bromodeoxyuridine/diagnostic use Carbonic Anhydrase Inhibitors Cell Division/physiology Drug Interactions Embryo, Mammalian/metabolism Embryonic and Fetal Development Female Hydrogen-Ion Concentration image processing, computer-assisted/methods Intracellular Fluid/metabolism Limb Buds/abnormalities Limb Buds/growth & development Limb Buds/metabolism Male Mesoderm Mice Mice, Inbred C57BL Muscle, Skeletal/metabolism Pregnancy

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Multi-voxel coding of stimuli, rules, and responses in human frontoparietal cortex

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NEUROimage 2011年第2期56卷 744-752页

作者： Woolgar, Alexandra Thompson, Russell Bor, Daniel Duncan, John MRC Cognit & Brain Sci Unit Cambridge CB2 7EF England

In human functional magnetic resonance imaging (fMRI), a characteristic pattern of frontal and parietal activity is produced by many different cognitive demands. Although frontoparietal cortex has been shown to represent a variety of task features in different contexts, little is known about detailed representation of different task features within and across different regions. We used multi-voxel pattern analysis (MVPA) of human fMRI data to assess the representational content of frontoparietal cortex in a simple stimulus-response task. Stimulus-response mapping rule was the most strongly represented task feature, significantly coded in a lateral frontal region surrounding the inferior frontal sulcus, a more ventral region including the anterior insula/frontal operculum, and the intraparietal sulcus. Next strongest was coding of the instruction cue (screen color) indicating which rule should be applied. Coding of individual stimuli and responses was weaker, approaching significance in a subset of regions. In line with recent single unit data, the results show a broad representation of task-relevant information across human frontoparietal cortex, with strong representation of a general rule or cognitive context, and weaker coding of individual stimulus/response instances. (C) 2010 Elsevier Inc. All rights reserved.

关键词： Brain Mapping/methods Brain Mapping/methods Female Frontal Lobe/physiology Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Male Parietal Lobe/physiology Pattern Recognition, Automated/methods Young Adult

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