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Alexandra Badea

Associate Professor in Radiology
Radiology
Box 3302 Duke University Medic, Durham, NC 27710
Center for in Vivo Microscopy, Room 139 Bryan Research Building, Durham, NC 27710

Selected Publications


Accelerated Brain Atrophy, Microstructural Decline and Connectopathy in Age-Related Macular Degeneration.

Journal Article Biomedicines · January 10, 2024 Age-related macular degeneration (AMD) has recently been linked to cognitive impairment. We hypothesized that AMD modifies the brain aging trajectory, and we conducted a longitudinal diffusion MRI study on 40 participants (20 with AMD and 20 controls) to r ... Full text Open Access Link to item Cite

Multivariate investigation of aging in mouse models expressing the Alzheimer's protective APOE2 allele: integrating cognitive metrics, brain imaging, and blood transcriptomics.

Journal Article Brain Struct Funct · January 2024 APOE allelic variation is critical in brain aging and Alzheimer's disease (AD). The APOE2 allele associated with cognitive resilience and neuroprotection against AD remains understudied. We employed a multipronged approach to characterize the transition fr ... Full text Link to item Cite

A Continuous Extension of Gene Set Enrichment Analysis Using the Likelihood Ratio Test Statistics Identifies Vascular Endothelial Growth Factor as a Candidate Pathway for Alzheimer's Disease via ITGA5.

Journal Article J Alzheimers Dis · 2024 BACKGROUND: Alzheimer's disease (AD) involves brain neuropathologies such as amyloid plaque and hyperphosphorylated tau tangles and is accompanied by cognitive decline. Identifying the biological mechanisms underlying disease onset and progression based on ... Full text Link to item Cite

A Continuous Extension of Gene Set Enrichment Analysis using the Likelihood Ratio Test Statistics Identifies VEGF as a Candidate Pathway for Alzheimer's disease.

Journal Article bioRxiv · August 26, 2023 BACKGROUND: Alzheimer's disease involves brain pathologies such as amyloid plaque depositions and hyperphosphorylated tau tangles and is accompanied by cognitive decline. Identifying the biological mechanisms underlying disease onset and progression based ... Full text Link to item Cite

Identifying vulnerable brain networks associated with Alzheimer's disease risk.

Journal Article Cereb Cortex · April 25, 2023 The selective vulnerability of brain networks in individuals at risk for Alzheimer's disease (AD) may help differentiate pathological from normal aging at asymptomatic stages, allowing the implementation of more effective interventions. We used a sample of ... Full text Link to item Cite

An Online Repository for Pre-Clinical Imaging Protocols (PIPs).

Journal Article Tomography (Ann Arbor, Mich.) · March 2023 Providing method descriptions that are more detailed than currently available in typical peer reviewed journals has been identified as an actionable area for improvement. In the biochemical and cell biology space, this need has been met through the creatio ... Full text Open Access Cite

Advanced photon counting CT imaging pipeline for cardiac phenotyping of apolipoprotein E mouse models.

Journal Article PLoS One · 2023 BACKGROUND: Cardiovascular disease (CVD) is associated with the apolipoprotein E (APOE) gene and lipid metabolism. This study aimed to develop an imaging-based pipeline to comprehensively assess cardiac structure and function in mouse models expressing dif ... Full text Link to item Cite

Automated multimodal segmentation of acute ischemic stroke lesions on clinical MR images.

Journal Article Magn Reson Imaging · October 2022 Magnetic resonance (MR) imaging (MRI) is commonly used to diagnose, assess and monitor stroke. Accurate and timely segmentation of stroke lesions provides the anatomico-structural information that can aid physicians in predicting prognosis, as well as in d ... Full text Open Access Link to item Cite

Anatomical and functional cardiac PCCT imaging pipeline for characterization of Apolipoprotein E mouse models

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2022 Non-invasive imaging strategies are essential in understanding the factors associated with the ongoing rise in cardiovascular disease (CVD) and Alzheimer’s disease (AD), and the possible interactions between these diseases. Our scientific premise is based ... Full text Cite

Absolute Winding Number Differentiates Mouse Spatial Navigation Strategies With Genetic Risk for Alzheimer's Disease.

Journal Article Front Neurosci · 2022 Spatial navigation and orientation are emerging as promising markers for altered cognition in prodromal Alzheimer's disease, and even in cognitively normal individuals at risk for Alzheimer's disease. The different APOE gene alleles confer various degrees ... Full text Link to item Cite

Corrigendum: Absolute winding number differentiates mouse spatial navigation strategies with genetic risk for Alzheimer's disease.

Journal Article Front Neurosci · 2022 [This corrects the article DOI: 10.3389/fnins.2022.848654.]. ... Full text Link to item Cite

Imaging Biomarkers for Alzheimer’s Disease Using Magnetic Resonance Microscopy

Chapter · January 1, 2022 A better understanding of how the brain's structure and connections give rise to motivation and behavior will lead to better therapies for psychiatric and neurological conditions, including neurodegenerative conditions such as Alzheimer's disease (AD). Mag ... Full text Cite

GLIS1 regulates trabecular meshwork function and intraocular pressure and is associated with glaucoma in humans.

Journal Article Nat Commun · August 12, 2021 Chronically elevated intraocular pressure (IOP) is the major risk factor of primary open-angle glaucoma, a leading cause of blindness. Dysfunction of the trabecular meshwork (TM), which controls the outflow of aqueous humor (AqH) from the anterior chamber, ... Full text Link to item Cite

Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways.

Journal Article Alzheimer's & dementia : the journal of the Alzheimer's Association · April 2021 IntroductionThe study of Alzheimer's disease (AD) has revealed biological pathways with implications for disease neuropathology and pathophysiology. These pathway-level effects may also be mediated by individual characteristics or covariates such ... Full text Cite

Microcephaly with altered cortical layering in GIT1 deficiency revealed by quantitative neuroimaging.

Journal Article Magn Reson Imaging · February 2021 G Protein-Coupled Receptor Kinase-Interacting Protein-1 (GIT1) regulates neuronal functions, including cell and axon migration and synapse formation and maintenance, and GIT1 knockout (KO) mice exhibit learning and memory deficits. We noted that male and f ... Full text Link to item Cite

Cerebral white matter connectivity, cognition, and age-related macular degeneration.

Journal Article Neuroimage Clin · 2021 Age-related macular degeneration (AMD) is a common retina disease associated with cognitive impairment in older adults. The mechanism(s) that account for the link between AMD and cognitive decline remain unclear. Here we aim to shed light on this issue by ... Full text Open Access Link to item Cite

AGE-RELATED MACULAR DEGENERATION AND THE AGING BRAIN

Conference INNOVATION IN AGING · 2021 Cite

β-Arrestin-Biased Allosteric Modulator of NTSR1 Selectively Attenuates Addictive Behaviors.

Journal Article Cell · June 11, 2020 Small molecule neurotensin receptor 1 (NTSR1) agonists have been pursued for more than 40 years as potential therapeutics for psychiatric disorders, including drug addiction. Clinical development of NTSR1 agonists has, however, been precluded by their seve ... Full text Link to item Cite

Accelerated Brain Atrophy, Microstructural Decline and Connectopathy in Age-Related Macular Degeneration.

Journal Article Biomedicines · January 10, 2024 Age-related macular degeneration (AMD) has recently been linked to cognitive impairment. We hypothesized that AMD modifies the brain aging trajectory, and we conducted a longitudinal diffusion MRI study on 40 participants (20 with AMD and 20 controls) to r ... Full text Open Access Link to item Cite

Multivariate investigation of aging in mouse models expressing the Alzheimer's protective APOE2 allele: integrating cognitive metrics, brain imaging, and blood transcriptomics.

Journal Article Brain Struct Funct · January 2024 APOE allelic variation is critical in brain aging and Alzheimer's disease (AD). The APOE2 allele associated with cognitive resilience and neuroprotection against AD remains understudied. We employed a multipronged approach to characterize the transition fr ... Full text Link to item Cite

A Continuous Extension of Gene Set Enrichment Analysis Using the Likelihood Ratio Test Statistics Identifies Vascular Endothelial Growth Factor as a Candidate Pathway for Alzheimer's Disease via ITGA5.

Journal Article J Alzheimers Dis · 2024 BACKGROUND: Alzheimer's disease (AD) involves brain neuropathologies such as amyloid plaque and hyperphosphorylated tau tangles and is accompanied by cognitive decline. Identifying the biological mechanisms underlying disease onset and progression based on ... Full text Link to item Cite

A Continuous Extension of Gene Set Enrichment Analysis using the Likelihood Ratio Test Statistics Identifies VEGF as a Candidate Pathway for Alzheimer's disease.

Journal Article bioRxiv · August 26, 2023 BACKGROUND: Alzheimer's disease involves brain pathologies such as amyloid plaque depositions and hyperphosphorylated tau tangles and is accompanied by cognitive decline. Identifying the biological mechanisms underlying disease onset and progression based ... Full text Link to item Cite

Identifying vulnerable brain networks associated with Alzheimer's disease risk.

Journal Article Cereb Cortex · April 25, 2023 The selective vulnerability of brain networks in individuals at risk for Alzheimer's disease (AD) may help differentiate pathological from normal aging at asymptomatic stages, allowing the implementation of more effective interventions. We used a sample of ... Full text Link to item Cite

An Online Repository for Pre-Clinical Imaging Protocols (PIPs).

Journal Article Tomography (Ann Arbor, Mich.) · March 2023 Providing method descriptions that are more detailed than currently available in typical peer reviewed journals has been identified as an actionable area for improvement. In the biochemical and cell biology space, this need has been met through the creatio ... Full text Open Access Cite

Advanced photon counting CT imaging pipeline for cardiac phenotyping of apolipoprotein E mouse models.

Journal Article PLoS One · 2023 BACKGROUND: Cardiovascular disease (CVD) is associated with the apolipoprotein E (APOE) gene and lipid metabolism. This study aimed to develop an imaging-based pipeline to comprehensively assess cardiac structure and function in mouse models expressing dif ... Full text Link to item Cite

Automated multimodal segmentation of acute ischemic stroke lesions on clinical MR images.

Journal Article Magn Reson Imaging · October 2022 Magnetic resonance (MR) imaging (MRI) is commonly used to diagnose, assess and monitor stroke. Accurate and timely segmentation of stroke lesions provides the anatomico-structural information that can aid physicians in predicting prognosis, as well as in d ... Full text Open Access Link to item Cite

Anatomical and functional cardiac PCCT imaging pipeline for characterization of Apolipoprotein E mouse models

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2022 Non-invasive imaging strategies are essential in understanding the factors associated with the ongoing rise in cardiovascular disease (CVD) and Alzheimer’s disease (AD), and the possible interactions between these diseases. Our scientific premise is based ... Full text Cite

Absolute Winding Number Differentiates Mouse Spatial Navigation Strategies With Genetic Risk for Alzheimer's Disease.

Journal Article Front Neurosci · 2022 Spatial navigation and orientation are emerging as promising markers for altered cognition in prodromal Alzheimer's disease, and even in cognitively normal individuals at risk for Alzheimer's disease. The different APOE gene alleles confer various degrees ... Full text Link to item Cite

Corrigendum: Absolute winding number differentiates mouse spatial navigation strategies with genetic risk for Alzheimer's disease.

Journal Article Front Neurosci · 2022 [This corrects the article DOI: 10.3389/fnins.2022.848654.]. ... Full text Link to item Cite

Imaging Biomarkers for Alzheimer’s Disease Using Magnetic Resonance Microscopy

Chapter · January 1, 2022 A better understanding of how the brain's structure and connections give rise to motivation and behavior will lead to better therapies for psychiatric and neurological conditions, including neurodegenerative conditions such as Alzheimer's disease (AD). Mag ... Full text Cite

GLIS1 regulates trabecular meshwork function and intraocular pressure and is associated with glaucoma in humans.

Journal Article Nat Commun · August 12, 2021 Chronically elevated intraocular pressure (IOP) is the major risk factor of primary open-angle glaucoma, a leading cause of blindness. Dysfunction of the trabecular meshwork (TM), which controls the outflow of aqueous humor (AqH) from the anterior chamber, ... Full text Link to item Cite

Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways.

Journal Article Alzheimer's & dementia : the journal of the Alzheimer's Association · April 2021 IntroductionThe study of Alzheimer's disease (AD) has revealed biological pathways with implications for disease neuropathology and pathophysiology. These pathway-level effects may also be mediated by individual characteristics or covariates such ... Full text Cite

Microcephaly with altered cortical layering in GIT1 deficiency revealed by quantitative neuroimaging.

Journal Article Magn Reson Imaging · February 2021 G Protein-Coupled Receptor Kinase-Interacting Protein-1 (GIT1) regulates neuronal functions, including cell and axon migration and synapse formation and maintenance, and GIT1 knockout (KO) mice exhibit learning and memory deficits. We noted that male and f ... Full text Link to item Cite

Cerebral white matter connectivity, cognition, and age-related macular degeneration.

Journal Article Neuroimage Clin · 2021 Age-related macular degeneration (AMD) is a common retina disease associated with cognitive impairment in older adults. The mechanism(s) that account for the link between AMD and cognitive decline remain unclear. Here we aim to shed light on this issue by ... Full text Open Access Link to item Cite

AGE-RELATED MACULAR DEGENERATION AND THE AGING BRAIN

Conference INNOVATION IN AGING · 2021 Cite

β-Arrestin-Biased Allosteric Modulator of NTSR1 Selectively Attenuates Addictive Behaviors.

Journal Article Cell · June 11, 2020 Small molecule neurotensin receptor 1 (NTSR1) agonists have been pursued for more than 40 years as potential therapeutics for psychiatric disorders, including drug addiction. Clinical development of NTSR1 agonists has, however, been precluded by their seve ... Full text Link to item Cite

Optimizing Diffusion Imaging Protocols for Structural Connectomics in Mouse Models of Neurological Conditions.

Journal Article Front Phys · April 2020 Network approaches provide sensitive biomarkers for neurological conditions, such as Alzheimer's disease (AD). Mouse models can help advance our understanding of underlying pathologies, by dissecting vulnerable circuits. While the mouse brain contains less ... Full text Link to item Cite

MRI-Based Deep Learning Segmentation and Radiomics of Sarcoma in Mice.

Journal Article Tomography · March 2020 Small-animal imaging is an essential tool that provides noninvasive, longitudinal insight into novel cancer therapies. However, considerable variability in image analysis techniques can lead to inconsistent results. We have developed quantitative imaging f ... Full text Open Access Link to item Cite

MRI-based radiomics of sarcomas in the preclinical arm of a Co-clinical trial

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2020 Radiomics provide an exciting approach to developing imaging biomarkers in the context of precision medicine. We focus on the preclinical arm of a co-clinical trial investigating synergy of immunotherapy combined with radiation therapy (RT) and surgical re ... Full text Cite

βII-spectrin promotes mouse brain connectivity through stabilizing axonal plasma membranes and enabling axonal organelle transport.

Journal Article Proc Natl Acad Sci U S A · July 30, 2019 βII-spectrin is the generally expressed member of the β-spectrin family of elongated polypeptides that form micrometer-scale networks associated with plasma membranes. We addressed in vivo functions of βII-spectrin in neurons by knockout of βII-spectrin in ... Full text Link to item Cite

ANK2 autism mutation targeting giant ankyrin-B promotes axon branching and ectopic connectivity.

Journal Article Proc Natl Acad Sci U S A · July 23, 2019 Giant ankyrin-B (ankB) is a neurospecific alternatively spliced variant of ANK2, a high-confidence autism spectrum disorder (ASD) gene. We report that a mouse model for human ASD mutation of giant ankB exhibits increased axonal branching in cultured neuron ... Full text Link to item Cite

Small Animal Multivariate Brain Analysis (SAMBA) - a High Throughput Pipeline with a Validation Framework.

Journal Article Neuroinformatics · July 2019 While many neuroscience questions aim to understand the human brain, much current knowledge has been gained using animal models, which replicate genetic, structural, and connectivity aspects of the human brain. While voxel-based analysis (VBA) of preclinic ... Full text Link to item Cite

Multivariate MR biomarkers better predict cognitive dysfunction in mouse models of Alzheimer's disease.

Journal Article Magn Reson Imaging · July 2019 To understand multifactorial conditions such as Alzheimer's disease (AD) we need brain signatures that predict the impact of multiple pathologies and their interactions. To help uncover the relationships between pathology affected brain circuits and cognit ... Full text Link to item Cite

Connectome Smoothing via Low-Rank Approximations.

Journal Article IEEE Trans Med Imaging · June 2019 In brain imaging and connectomics, the study of brain networks, estimating the mean of a population of graphs based on a sample is a core problem. Often, this problem is especially difficult because the sample or cohort size is relatively small, sometimes ... Full text Link to item Cite

Applications of 3D printing in small animal magnetic resonance imaging.

Journal Article J Med Imaging (Bellingham) · April 2019 Three-dimensional (3D) printing has significantly impacted the quality, efficiency, and reproducibility of preclinical magnetic resonance imaging. It has vastly expanded the ability to produce MR-compatible parts that readily permit customization of animal ... Full text Link to item Cite

Magnetic resonance imaging of mouse brain networks plasticity following motor learning.

Journal Article PLoS One · 2019 We do not have a full understanding of the mechanisms underlying plasticity in the human brain. Mouse models have well controlled environments and genetics, and provide tools to help dissect the mechanisms underlying the observed responses to therapies dev ... Full text Link to item Cite

Identifying Vulnerable Brain Networks in Mouse Models of Genetic Risk Factors for Late Onset Alzheimer's Disease.

Journal Article Front Neuroinform · 2019 The major genetic risk for late onset Alzheimer's disease has been associated with the presence of APOE4 alleles. However, the impact of different APOE alleles on the brain aging trajectory, and how they interact with the brain local environment in a sex s ... Full text Link to item Cite

Whole mouse brain structural connectomics using magnetic resonance histology.

Journal Article Brain Struct Funct · December 2018 Diffusion tensor histology holds great promise for quantitative characterization of structural connectivity in mouse models of neurological and psychiatric conditions. There has been extensive study in both the clinical and preclinical domains on the compl ... Full text Link to item Cite

Diffusion tensor imaging using multiple coils for mouse brain connectomics.

Journal Article NMR Biomed · June 2018 The correlation between brain connectivity and psychiatric or neurological diseases has intensified efforts to develop brain connectivity mapping techniques on mouse models of human disease. The neural architecture of mouse brain specimens can be shown non ... Full text Link to item Cite

Repeated mild blast exposure in young adult rats results in dynamic and persistent microstructural changes in the brain.

Journal Article Neuroimage Clin · 2018 A history of mild traumatic brain injury (mTBI), particularly repeated mTBI (rmTBI), has been identified as a risk factor for late-onset neurodegenerative conditions. The mild and transient nature of early symptoms often impedes diagnosis in young adults w ... Full text Link to item Cite

The organization of frequency and binaural cues in the gerbil inferior colliculus.

Journal Article J Comp Neurol · June 15, 2017 The inferior colliculus (IC) is the common target of separate pathways that transmit different types of auditory information. Beyond tonotopy, little is known about the organization of response properties within the 3-dimensional layout of the auditory mid ... Full text Link to item Cite

The fornix provides multiple biomarkers to characterize circuit disruption in a mouse model of Alzheimer's disease.

Journal Article Neuroimage · November 15, 2016 Multivariate biomarkers are needed for detecting Alzheimer's disease (AD), understanding its etiology, and quantifying the effect of therapies. Mouse models provide opportunities to study characteristics of AD in well-controlled environments that can help ... Full text Link to item Cite

Mouse model of rare TOR1A variant found in sporadic focal dystonia impairs domains affected in DYT1 dystonia patients and animal models.

Journal Article Neurobiol Dis · September 2016 Rare de novo mutations in genes associated with inherited Mendelian disorders are potential contributors to sporadic disease. DYT1 dystonia is an autosomal dominant, early-onset, generalized dystonia associated with an in-frame, trinucleotide deletion (n. ... Full text Link to item Cite

Altered mGluR5-Homer scaffolds and corticostriatal connectivity in a Shank3 complete knockout model of autism.

Journal Article Nat Commun · May 10, 2016 Human neuroimaging studies suggest that aberrant neural connectivity underlies behavioural deficits in autism spectrum disorders (ASDs), but the molecular and neural circuit mechanisms underlying ASDs remain elusive. Here, we describe a complete knockout m ... Full text Open Access Link to item Cite

Image-processing pipelines: Applications in magnetic resonance histology

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · January 1, 2016 Image processing has become ubiquitous in imaging research - so ubiquitous that it is easy to loose track of how diverse this processing has become. The Duke Center for In Vivo Microscopy has pioneered the development of Magnetic Resonance Histology (MRH), ... Full text Cite

A Diffusion MRI Tractography Connectome of the Mouse Brain and Comparison with Neuronal Tracer Data.

Journal Article Cereb Cortex · November 2015 Interest in structural brain connectivity has grown with the understanding that abnormal neural connections may play a role in neurologic and psychiatric diseases. Small animal connectivity mapping techniques are particularly important for identifying aber ... Full text Open Access Link to item Cite

A diffusion tensor MRI atlas of the postmortem rhesus macaque brain.

Journal Article Neuroimage · August 15, 2015 The rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate for modeling the structure and function of the brain. Brain atlases, and particularly those based on magnetic resonance imaging (MRI), have become important tools for understandin ... Full text Link to item Cite

Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas.

Journal Article eNeuro · 2015 Simultaneous neural recordings taken from multiple areas of the rodent brain are garnering growing interest due to the insight they can provide about spatially distributed neural circuitry. The promise of such recordings has inspired great progress in meth ... Full text Open Access Link to item Cite

A PIK3C3-ankyrin-B-dynactin pathway promotes axonal growth and multiorganelle transport.

Journal Article J Cell Biol · December 22, 2014 Axon growth requires long-range transport of organelles, but how these cargoes recruit their motors and how their traffic is regulated are not fully resolved. In this paper, we identify a new pathway based on the class III PI3-kinase (PIK3C3), ankyrin-B (A ... Full text Link to item Cite

Investigating the tradeoffs between spatial resolution and diffusion sampling for brain mapping with diffusion tractography: time well spent?

Journal Article Hum Brain Mapp · November 2014 Interest in mapping white matter pathways in the brain has peaked with the recognition that altered brain connectivity may contribute to a variety of neurologic and psychiatric diseases. Diffusion tractography has emerged as a popular method for postmortem ... Full text Link to item Cite

Magnetic resonance histology—Applications in toxicology

Conference Toxicology Letters · September 2014 Full text Cite

Quantitative mapping of trimethyltin injury in the rat brain using magnetic resonance histology.

Journal Article Neurotoxicology · May 2014 The growing exposure to chemicals in our environment and the increasing concern over their impact on health have elevated the need for new methods for surveying the detrimental effects of these compounds. Today's gold standard for assessing the effects of ... Full text Open Access Link to item Cite

Transcript co-variance with Nestin in two mouse genetic reference populations identifies Lef1 as a novel candidate regulator of neural precursor cell proliferation in the adult hippocampus.

Journal Article Front Neurosci · 2014 Adult neurogenesis, the lifelong production of new neurons in the adult brain, is under complex genetic control but many of the genes involved remain to be identified. In this study, we have integrated publicly available gene expression data from the BXD a ... Full text Link to item Cite

Constructing a 4D murine cardiac micro-CT atlas for automated segmentation and phenotyping applications

Journal Article Progress in Biomedical Optics and Imaging - Proceedings of SPIE · June 3, 2013 A number of investigators have demonstrated the potential of preclinical micro-CT in characterizing cardiovascular disease in mouse models. One major hurdle to advancing this approach is the extensive user interaction required to derive quantitative metric ... Full text Cite

A quantitative magnetic resonance histology atlas of postnatal rat brain development with regional estimates of growth and variability.

Journal Article Neuroimage · May 1, 2013 There has been growing interest in the role of postnatal brain development in the etiology of several neurologic diseases. The rat has long been recognized as a powerful model system for studying neuropathology and the safety of pharmacologic treatments. H ... Full text Link to item Cite

Magnetic resonance microscopy.

Journal Article Stud Health Technol Inform · 2013 MRI, one of the major clinical imaging modalities, has gained an important role in studying small animal models, e.g., rats and mice. But imaging rodents comes with challenges, since the image resolution needs to be ~ 3000-times higher to resolve anatomica ... Link to item Cite

Quantitative mouse brain phenotyping based on single and multispectral MR protocols.

Journal Article Neuroimage · November 15, 2012 Sophisticated image analysis methods have been developed for the human brain, but such tools still need to be adapted and optimized for quantitative small animal imaging. We propose a framework for quantitative anatomical phenotyping in mouse models of neu ... Full text Link to item Cite

Registration-based segmentation of murine 4D cardiac micro-CT data using symmetric normalization.

Journal Article Phys Med Biol · October 7, 2012 Micro-CT can play an important role in preclinical studies of cardiovascular disease because of its high spatial and temporal resolution. Quantitative analysis of 4D cardiac images requires segmentation of the cardiac chambers at each time point, an extrem ... Full text Link to item Cite

Small animal imaging with magnetic resonance microscopy

Journal Article ILAR Journal · September 11, 2012 Small animal magnetic resonance microscopy (MRM) has evolved significantly from testing the boundaries of imaging physics to its expanding use today as a tool in noninvasive biomedical investigations. MRM now increasingly provides functional information ab ... Cite

A multidimensional magnetic resonance histology atlas of the Wistar rat brain.

Journal Article Neuroimage · September 2012 We have produced a multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). This MR atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between h ... Full text Link to item Cite

A prior feature SVM-MRF based method for mouse brain segmentation.

Journal Article Neuroimage · February 1, 2012 Featured Publication We introduce an automated method, called prior feature Support Vector Machine-Markov Random Field (pSVMRF), to segment three-dimensional mouse brain Magnetic Resonance Microscopy (MRM) images. Our earlier work, extended MRF (eMRF) integrated Support Vector ... Full text Link to item Cite

Magnetic resonance microscopy.

Journal Article Anal Cell Pathol (Amst) · 2012 Full text Open Access Link to item Cite

Identifying human disease genes through cross-species gene mapping of evolutionary conserved processes.

Journal Article PLoS One · May 4, 2011 Featured Publication BACKGROUND: Understanding complex networks that modulate development in humans is hampered by genetic and phenotypic heterogeneity within and between populations. Here we present a method that exploits natural variation in highly diverse mouse genetic refe ... Full text Link to item Cite

A symmetrical Waxholm canonical mouse brain for NeuroMaps.

Journal Article J Neurosci Methods · February 15, 2011 Featured Publication NeuroMaps (2010) is a Web-based application that enables investigators to map data from macaque studies to a canonical atlas of the macaque brain. It currently serves as an image processor enabling them to create figures suitable for publication, presentat ... Full text Link to item Cite

Quantitative neuromorphometry using magnetic resonance histology.

Journal Article Toxicol Pathol · January 2011 Featured Publication Magnetic resonance imaging (MRI), now common in the clinical domain, has been adapted for use by the neuropathologist by increasing the spatial resolution over 100,000 times what is common in human clinical imaging. This increase in spatial resolution has ... Full text Link to item Cite

Waxholm space: an image-based reference for coordinating mouse brain research.

Journal Article Neuroimage · November 1, 2010 Featured Publication 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 dif ... Full text Link to item Cite

Remote sites of structural atrophy predict later amyloid formation in a mouse model of Alzheimer's disease.

Journal Article Neuroimage · April 1, 2010 Featured Publication Magnetic resonance (MR) imaging can provide a longitudinal view of neurological disease through repeated imaging of patients at successive stages of impairment. Until recently, the difficulty of manual delineation has limited volumetric analyses of MR data ... Full text Link to item Cite

Genetic dissection of the mouse CNS using magnetic resonance microscopy.

Journal Article Curr Opin Neurol · August 2009 Featured Publication PURPOSE OF REVIEW: Advances in magnetic resonance microscopy (MRM) make it practical to map gene variants responsible for structural variation in brains of many species, including mice and humans. We review results of a systematic genetic analysis of MRM d ... Full text Link to item Cite

Automated segmentation of mouse brain images using extended MRF.

Journal Article Neuroimage · July 1, 2009 Featured Publication We introduce an automated segmentation method, extended Markov random field (eMRF), to classify 21 neuroanatomical structures of mouse brain based on three dimensional (3D) magnetic resonance images (MRI). The image data are multispectral: T2-weighted, pro ... Full text Link to item Cite

Genetic dissection of the mouse brain using high-field magnetic resonance microscopy.

Journal Article Neuroimage · May 1, 2009 Featured Publication Magnetic resonance (MR) imaging has demonstrated that variation in brain structure is associated with differences in behavior and disease state. However, it has rarely been practical to prospectively test causal models that link anatomical and functional d ... Full text Link to item Cite

Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy.

Journal Article Neuroimage · January 1, 2008 Featured Publication Magnetic resonance microscopy (MRM) has created new approaches for high-throughput morphological phenotyping of mouse models of diseases. Transgenic and knockout mice serve as a test bed for validating hypotheses that link genotype to the phenotype of dise ... Full text Link to item Cite

Small animal imaging with magnetic resonance microscopy.

Journal Article ILAR J · 2008 Featured Publication Small animal magnetic resonance microscopy (MRM) has evolved significantly from testing the boundaries of imaging physics to its expanding use today as a tool in noninvasive biomedical investigations. MRM now increasingly provides functional information ab ... Full text Link to item Cite

Morphometric analysis of the C57BL/6J mouse brain.

Journal Article Neuroimage · September 1, 2007 Featured Publication Magnetic resonance microscopy (MRM), when used in conjunction with active staining, can produce high-resolution, high-contrast images of the mouse brain. Using MRM, we imaged in situ the fixed, actively stained brains of C57BL/6J mice in order to character ... Full text Link to item Cite

High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology.

Journal Article Neuroimage · August 1, 2007 Featured Publication The Mouse Biomedical Informatics Research Network (MBIRN) has been established to integrate imaging studies of the mouse brain ranging from three-dimensional (3D) studies of the whole brain to focused regions at a sub-cellular scale. Magnetic resonance (MR ... Full text Link to item Cite

Neuroanatomical phenotypes in the reeler mouse.

Journal Article Neuroimage · February 15, 2007 Featured Publication The reeler mouse (Reln) has been proposed as a neurodevelopmental model for certain neurological and psychiatric conditions and has been studied by qualitative histochemistry and electron microscopy. Using magnetic resonance microscopy (MRM), we have quant ... Full text Link to item Cite

Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain.

Journal Article Neuroimage · August 15, 2005 Featured Publication We present the automated segmentation of magnetic resonance microscopy (MRM) images of the C57BL/6J mouse brain into 21 neuroanatomical structures, including the ventricular system, corpus callosum, hippocampus, caudate putamen, inferior colliculus, intern ... Full text Link to item Cite

Utilizing MRI information to estimate F18-FDG distributions in rat flank tumors

Conference IEEE Nuclear Science Symposium Conference Record · December 1, 2004 This paper investigates the potential of magnetic resonance imaging (MRI) to improve the estimation of within-tumor variations in F18-FDG concentration. An image model is described for incorporating MRI images into positron emission tomography (PET) and si ... Cite

Surface visualization of electromagnetic brain activity.

Journal Article J Neurosci Methods · August 15, 2003 Featured Publication Advances in hardware and software have made possible the reconstruction of brain activity from non-invasive electrophysiological measurements over a large part of the brain. The appreciation of the information content in the data is enhanced when relevant ... Full text Link to item Cite