Scholars@Duke
G. Allan Johnson

G. Allan Johnson

Charles E. Putman University Distinguished Professor of Radiology
Radiology
gjohnson@duke.edu
Box 3302 Med Ctr, Durham, NC 27710
141D Bryan Neuroscience Bldg, Research Drive, Durham, NC 27710
Office hours 8:30 AM-5:00 PM and by appointment.  

Featured Works

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

Journal article Cereb Cortex · November 2015 Featured Work 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 Featured Work 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

Postmortem diffusion MRI of the human brainstem and thalamus for deep brain stimulator electrode localization.

Journal article Hum Brain Mapp · August 2015 Featured Work Deep brain stimulation (DBS) is an established surgical therapy for medically refractory tremor disorders including essential tremor (ET) and is currently under investigation for use in a variety of other neurologic and psychiatric disorders. There is grow ... Full text Link to item Cite

Magnetic resonance histology.

Journal article J Magn Reson Imaging · July 2015 Featured Work Full text Link to item Cite

An MRI/DTI Atlas of the Rat Brain

Book · May 28, 2015 Featured Work MRI/DTI Atlas of the Rat Brain offers two major enhancements when compared with earlier attempts to make MRI/DTI rat brain atlases. First, the spatial resolution at 25μm is considerably higher than previous data published. Secondly, the comprehensive set o ... Cite

4D MRI of polycystic kidneys from rapamycin-treated Glis3-deficient mice.

Journal article NMR Biomed · May 2015 Featured Work Polycystic kidney disease (PKD) is a life-threatening disease that leads to a grotesque enlargement of the kidney and significant loss of function. Several imaging studies with MRI have demonstrated that cyst size in polycystic kidneys can determine diseas ... Full text Link to item Cite

Dynamic contrast-enhanced MR microscopy identifies regions of therapeutic response in a preclinical model of colorectal adenocarcinoma.

Journal article Med Phys · May 2015 Featured Work PURPOSE: A typical dynamic contrast-enhanced (DCE)-MRI study often compares the derived pharmacokinetic parameters on manually selected tumor regions or over the entire tumor volume. These measurements include domains where the interpretation of the biomar ... Full text Link to item Cite

Susceptibility tensor imaging of the kidney and its microstructural underpinnings.

Journal article Magn Reson Med · March 2015 Featured Work PURPOSE: The purpose of this study was to determine whether susceptibility tensor imaging (STI) could overcome limitations of current techniques to detect tubules throughout the kidney. METHODS: Normal mouse kidneys (n = 4) were imaged at 9.4T using a thre ... Full text Link to item Cite

Addendum to “Waxholm Space atlas of the Sprague Dawley rat brain” [NeuroImage 97 (2014) 374-386].

Journal article Neuroimage · January 15, 2015 Featured Work The main focus of our original article was to describe the anatomical delineations constituting the first version of the WHS Sprague Dawley atlas, apply the Waxholm Space coordinate system, and publish the associated MRI/DTI template and segmentation volum ... 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 Featured Work 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

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 Featured Work 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

Four-dimensional MRI of renal function in the developing mouse.

Journal article NMR Biomed · September 2014 Featured Work The major roles of filtration, metabolism and high blood flow make the kidney highly vulnerable to drug-induced toxicity and other renal injuries. A method to follow kidney function is essential for the early screening of toxicity and malformations. In thi ... Full text Link to item Cite

Magnetic resonance histology—Applications in toxicology

Conference Toxicology Letters · September 2014 Featured Work Full text Cite

Waxholm Space atlas of the Sprague Dawley rat brain.

Journal article Neuroimage · August 15, 2014 Featured Work Three-dimensional digital brain atlases represent an important new generation of neuroinformatics tools for understanding complex brain anatomy, assigning location to experimental data, and planning of experiments. We have acquired a microscopic resolution ... Full text Link to item Cite

Diffusion tensor imaging reveals white matter injury in a rat model of repetitive blast-induced traumatic brain injury.

Journal article J Neurotrauma · May 15, 2014 Featured Work Blast-induced traumatic brain injury (bTBI) is one of the most common combat-related injuries seen in U.S. military personnel, yet relatively little is known about the underlying mechanisms of injury. In particular, the effects of the primary blast pressur ... Full text Link to item Cite

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

Journal article Neurotoxicology · May 2014 Featured Work 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

Semi-automated 3D segmentation of major tracts in the rat brain: comparing DTI with standard histological methods.

Journal article Brain Struct Funct · March 2014 Featured Work Researchers working with rodent models of neurological disease often require an accurate map of the anatomical organization of the white matter of the rodent brain. With the increasing popularity of small animal MRI techniques, including diffusion tensor i ... Full text Link to item Cite

Diffusion tensor magnetic resonance histology reveals microstructural changes in the developing rat brain.

Journal article Neuroimage · October 1, 2013 Featured Work The postnatal period is a remarkably dynamic phase of brain growth and development characterized by large-scale macrostructural changes, as well as dramatic microstructural changes, including myelination and cortical layering. This crucial period of neurod ... Full text Link to item Cite

Magnetic resonance histology: cool images- but who cares?

Journal article TOXICOLOGY LETTERS · August 28, 2013 Featured Work Full text Link to item Cite

The utility of micro-CT and MRI in the assessment of longitudinal growth of liver metastases in a preclinical model of colon carcinoma.

Journal article Acad Radiol · April 2013 Featured Work RATIONALE AND OBJECTIVES: Liver is a common site for distal metastases in colon and rectal cancer. Numerous clinical studies have analyzed the relative merits of different imaging modalities for detection of liver metastases. Several exciting new therapies ... Full text Link to item Cite

An ontology-based segmentation scheme for tracking postnatal changes in the developing rodent brain with MRI.

Journal article Neuroimage · February 15, 2013 Featured Work The postnatal period of neurodevelopment has been implicated in a number of brain disorders including autism and schizophrenia. Rodent models have proven to be invaluable in advancing our understanding of the human brain, and will almost certainly play a p ... Full text Link to item Cite

A comparison of radial keyhole strategies for high spatial and temporal resolution 4D contrast-enhanced MRI in small animal tumor models.

Journal article Med Phys · February 2013 Featured Work PURPOSE: Dynamic contrast-enhanced (DCE) MRI has been widely used as a quantitative imaging method for monitoring tumor response to therapy. The simultaneous challenges of increasing temporal and spatial resolution in a setting where the signal from the mu ... Full text Link to item Cite

Magnetic resonance microscopy.

Journal article Stud Health Technol Inform · 2013 Featured Work 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 Featured Work 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

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

Journal article Neuroimage · September 2012 Featured Work 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

3D fiber tractography with susceptibility tensor imaging.

Journal article Neuroimage · January 16, 2012 Featured Work Gradient-echo MRI has revealed anisotropic magnetic susceptibility in the brain white matter. This magnetic susceptibility anisotropy can be measured and characterized with susceptibility tensor imaging (STI). In this study, a method of fiber tractography ... Full text Link to item Cite

4D micro-CT using fast prospective gating.

Journal article Phys Med Biol · January 7, 2012 Featured Work Micro-CT is currently used in preclinical studies to provide anatomical information. But, there is also significant interest in using this technology to obtain functional information. We report here a new sampling strategy for 4D micro-CT for functional ca ... Full text Link to item Cite

Magnetic resonance microscopy.

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

Ethanol-induced face-brain dysmorphology patterns are correlative and exposure-stage dependent.

Journal article PLoS One · 2012 Featured Work Prenatal ethanol exposure is the leading preventable cause of congenital mental disability. Whereas a diagnosis of fetal alcohol syndrome (FAS) requires identification of a specific pattern of craniofacial dysmorphology, most individuals with behavioral an ... Full text Link to item Cite

Population-averaged diffusion tensor imaging atlas of the Sprague Dawley rat brain.

Journal article Neuroimage · October 15, 2011 Featured Work Rats are widely used in experimental neurobiological research, and rat brain atlases are important resources for identifying brain regions in the context of experimental microsurgery, tissue sampling, and neuroimaging, as well as comparison of findings acr ... Full text Link to item Cite

High-field (9.4 T) MRI of brain dysmyelination by quantitative mapping of magnetic susceptibility.

Journal article Neuroimage · June 1, 2011 Featured Work The multilayered myelin sheath wrapping around nerve axons is essential for proper functioning of the central nervous system. Abnormal myelination leads to a wide range of neurological diseases and developmental disorders. Non-invasive imaging of myelin co ... Full text Link to item Cite

A symmetrical Waxholm canonical mouse brain for NeuroMaps.

Journal article J Neurosci Methods · February 15, 2011 Featured Work 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

Digital atlasing and standardization in the mouse brain.

Journal article PLoS Comput Biol · February 3, 2011 Featured Work Full text Link to item Cite

Quantitative neuromorphometry using magnetic resonance histology.

Journal article Toxicol Pathol · January 2011 Featured Work 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 Work 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

Multishot PROPELLER for high-field preclinical MRI.

Journal article Magn Reson Med · July 2010 Featured Work With the development of numerous mouse models of cancer, there is a tremendous need for an appropriate imaging technique to study the disease evolution. High-field T(2)-weighted imaging using PROPELLER (Periodically Rotated Overlapping ParallEL Lines with ... Full text Link to item Cite

Microscopic diffusion tensor imaging of the mouse brain.

Journal article Neuroimage · April 1, 2010 Featured Work Diffusion tensor imaging (DTI) data at 43 mum isotropic resolution has been acquired on the intact adult mouse brain in 28-h scan time by using a streamlined protocol, including specimen fixation and staining, image acquisition, reconstruction, post-proces ... 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 Work 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

Ventilation/perfusion imaging in a rat model of airway obstruction.

Journal article Magn Reson Med · March 2010 Featured Work The global increase in asthma, chronic obstructive pulmonary disease, and other pulmonary diseases has stimulated interest in preclinical rat models of pulmonary disease. Imaging methods for study of these models is particularly appealing since the results ... Full text Link to item Cite

Active staining of mouse embryos for magnetic resonance microscopy.

Journal article Methods Mol Biol · 2010 Featured Work Magnetic resonance histology (MRH) has found considerable application in structural phenotyping in the mouse embryo. MRH employs the same fundamental principles as clinical MRI, albeit with spatial resolution up to six orders of magnitude higher than that ... Full text Link to item Cite

Genetic dissection of the mouse CNS using magnetic resonance microscopy.

Journal article Curr Opin Neurol · August 2009 Featured Work 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 the actively stained mouse brain using multi-spectral MR microscopy.

Journal article Neuroimage · January 1, 2008 Featured Work 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

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

Journal article Neuroimage · August 1, 2007 Featured Work 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

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

Journal article Neuroimage · August 15, 2005 Featured Work 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

Image based phenotyping: The visible mouse

Journal article FASEB JOURNAL · March 22, 2002 Featured Work Link to item Cite

Morphologic phenotyping with MR microscopy: the visible mouse.

Journal article Radiology · March 2002 Featured Work A method for rapid morphologic phenotyping is demonstrated by using magnetic resonance microscopy. Whole fixed C57BL/6J mice were imaged at 110-microm isotropic resolution; limited volumes of the intact specimen, at 50-microm isotropic resolution; and isol ... Full text Link to item Cite

An engineering approach to image-based phenotyping

Conference 2002 IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING, PROCEEDINGS · 2002 Featured Work Link to item Cite

Histology by magnetic resonance microscopy.

Journal article Magn Reson Q · March 1993 Featured Work Magnetic resonance microscopy (MRM) has advanced from a technical challenge to a practical tool in a wide range of basic sciences. This article focuses on the use of MRM as a tool for histological studies. The technical challenges of limited signal to nois ... Link to item Cite

Three-dimensional MRI microscopy of the normal rat brain.

Journal article Magn Reson Med · April 1987 Featured Work Magnetic resonance imaging techniques have been developed to enable imaging of the live rat brain with thin (1.2-mm) slices and microscopic pixels (115 X 115 microns). Signal-to-noise ratios high enough to realize the microscopic resolution are obtained wi ... Full text Link to item Cite

Nuclear magnetic resonance imaging at microscopic resolution

Journal article Journal of Magnetic Resonance (1969) · 1986 Featured Work Resolution limits in NMR imaging are imposed by bandwidth considerations, available magnetic gradients for spatial encoding, and signal to noise. This work reports modification of a clinical NMR imaging device with picture elements of 500 × 500 × 5000 μm t ... Cite