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Postal mailing address for all staff:

Center for In Vivo Microscopy
Box 3302, Duke University Medical Center
Durham, NC 27710    Courier address: 311 Research Drive, Durham, NC 27710

Main phone: 919 684-7755    fax: 919 684-7158

td>Lucy has over 20 years of system/network administration experience. She manages and supports all CIVM IT activities including all of the Center's computers and software. She provides technical assistance to users within and outside of our lab.

DIRECTOR - G. ALLAN JOHNSON PhD

Charles E. Putman University Professor of Radiology; Professor of Biomedical Engineering and Physics
919 684-7754    gjohnson@duke.edu
Dr. Johnson is Director of the Center for In Vivo Microscopy, an NIH/NIBIB-funded National Biomedical Technology Resource Center (P41 EB0015897), now into 25+ years of funding. He received a PhD in Physics from Duke University in 1974 in electron spin resonance under Walter Gordy and has been in Duke Radiology since 1974, where he is currently Director of Diagnostic Physics. He holds joint appointments in Radiology, Physics, and Biomedical Engineering as the Charles E. Putman University Professor, and he is co-author of 300+ peer-reviewed papers.
 
Dr. Johnson's research involves MR histology (MRH), the application of MR microscopy to study tissue architecture. Using MRH for morphologic phenotyping in the mouse was 1st suggested by Dr. Johnson and colleagues in Radiology 2002. A publication of the Waxholm Space (WHS) atlas of the C57BL mouse brain was created in conjunction with the International Neuroinformatics Coordinating Facility (INCF) digital brain atlasing program to be the center of a digital atlasing architecture that shares mouse brain data with the scientific research community. Work on brain atlases has continued (see publications), and our shared data provide access to other data sets.
 
MyNCBI link to publications
 

FACULTY

 
ALEXANDRA BADEA PhD - Assistant Professor - Radiology AlexandraBadea
919 684-7654    alexandra.badea@duke.edu
As director of CIVM's visualization core, Alexandra's research focuses on image analysis techniques to comprehensively characterize brain morphology. Her interests include phenotyping mouse neuroanatomy from fixed specimens to live-animal imaging, and uncovering links between structural changes in disease models, genetic bases, and environmental factors that modulate those changes.
 
Alex generates methods and tools for comprehensive phenotyping, including imaging protocols for optimal contrast, brain segmentation, registration, statistical analysis, and atlasing. Goals are to quantify changes during normal development, aging, disease progression, and to assess effects of treatment in a quantitative fashion. This interdisciplinary approach combines imaging data with behavioral and genetic tools, which can lead to translational studies. Alex encourages and mentors women who are interested in science careers to learn about imaging by working with us on projects, sometimes during the summer, or often within their undergraduate or graduate programs. See Training.
MyNCBI link to Alex's publications, and her Duke web page
   
CRISTIAN BADEA PhD - Associate Professor - Radiology, Biomedical Engineering, Medical Physics and Associate Director of CIVM
919 684-7509   cristian.badea@duke.edu
Cris directs the CIVM CT core, with research that includes x-ray-based methods for small animal morphological and functional imaging. His research incorporates CT, digital tomosynthesis, digital subtraction angiography, and image reconstruction algorithms. He designs and implements new systems and methods for in vivo dynamic high-resolution imaging using micro-CT and x-ray angiography for mouse cardiac phenotyping. The unique micro-CT system he developed at CIVM was used to produce the 1st in vivo cine micro-CT of the mouse heart with isotropic resolution of 100 microns and temporal resolution of 10 ms. Cristian's research also covers quantitative 4D tumor imaging using digital subtraction angiography and micro-CT.
MyNCBI link to Cristian's publications, and his Duke web page
   
BASTIAAN DRIEHUYS PhD - Professor - Radiology, Biomedical Engineering, Medical Physics
919 684-7786   bastiaan.driehuys@duke.edu
Bas is in charge of CIVM's MR hyperpolarized gases core. His ongoing research involves deploying and validating MR-based imaging biomarkers of pulmonary function and structure in a variety of disease areas. He helped introduce the field of hyperpolarized (HP) gas MRI, including the 1st animal and human studies using 3He and 129Xe. His research has turned towards exploiting solubility and chemical shifts of 129Xe to evaluate regional pulmonary gas exchange, and his team has applied that technology to patients with idiopathic pulmonary fibrosis and identified both unique spectroscopic and imaging signatures of disease.
 
With industry and academic experience, Bas' interests span not only attacking the basic physics problems of these gases, but in their large-scale expansion and application to biomedical problems. His integrated team combines atomic physics research, polarizer engineering, and developing MR hardware and techniques to get maximum signal and contrast. His efforts have now expanded into the clinical arena.
See the Xenon Shared Resource Facilty, and MyNCBI link to Bas' publications.
   
   
LAURENCE HEDLUND PhD - Professor Emeritus of Radiology
919 684-7767   laurence.hedlund@duke.edu
Dr. Hedlund is retired as a Professor of Radiology, but now has the status of Professor Emeritus.

 

Larry still works with CIVM, and continues to assist with Institutional Animal Care and Use Committee (IACUC) certification for live animal studies. He also helps develop physiologic monitoring and support technologies used for live animal imaging.
 
PubMed to Larry's publications.
 
 
 
 
 
   
JOHN NOULS PhD - Assistant Research Professor - Radiology JohnNouls
919 684-7769   john.nouls@duke.edu
 
John's work concentrates on multi-modality imaging. With his background in MRI, he runs our 7T Bruker magnet. He is skilled in all aspects of MR engineering, image processing and quantification, and small animal handling for live imaging studies. His skills include:
  • Developing high-throughput systems for imaging mice consistently using different modalities
  • Developing custom 3D-printed animal beds for reliable positioning of mice, while preventing even minimal animal motion or trauma. These custom beds have allowed steady, repeatable image acquisition, successful the 1st time, even in severely compromised animals.
  • Consistency of animal positioning has made it possible to observe very subtle features or changes during high-resolution mouse brain imaging
MyNCBI link to John's publications.

 

FACULTY at other locations

 
  • MARTIN FISCHER PhD - Associate Research Professor of Chemistry
  • WARREN S WARREN PhD - James B. Duke Professor of Chemistry, Director of the Center for Molecular and Biomolecular Imaging, Professor of Physics, Radiology, and Biomedical Engineering
  • JUNJIE YAO - Assistant Professor of Biomedical Engineering

 

STAFF

 
TATIANA ALEXANDER - Administrative Assistant tatiana
919 684-7877   tatiana.johnson@duke.edu
 
 

 

 

Tatiana takes care of the many administrative and financial tasks needed to keep the Center for In Vivo Microscopy running smoothly.
 
 
 
ROBERT "BJ" ANDERSON PhD - Post-doctoral Associate BJ
919 684-7793   robert.j.anderson@dm.duke.edu
 
BJ received his PhD in physics at UNC-Chapel Hill, where he developed H1 NMR techniques to study the hydrogen storage properties of various carbonaceous nanomaterials.
 
BJ works with Dr. Alexandra Badea implementing the registration and segmentation pipeline, focusing on optimizing accuracy and runtime of these processes. His current research interests include exploring ways to integrate advanced image-processing and machine-learning algorithms into the pipelines, and applying his experience with custom MR pulses to various CIVM projects.
 
 
   
DARIN CLARK PhD- Post-doctoral Associate Darin
919 684-7507   darin.clark@duke.edu
 
Darin defended his dissertation on "An Integrated Framework for Spectral and Temporal X-ray CT " in November 2015, and stayed on as a Post-doctoral Associate to continue his work under direction of Dr. Cristian Badea. His research includes 4D bilateral filtration of cardiac CT data, which provides a powerful denoising and regularization scheme for post-processing 4D cardiac micro-CT data in the mouse.
 
Darin's work continues to contribute to many of our CT technological advances, collaborations, and resulting publications.
 
PubMed link to Darin's publications
 
   
GARY COFER - MR Operations Manager gary
919 684-7677   gary.cofer@dm.duke.edu
 
Gary's multi-faceted functions at CIVM include the physical, electronic, and software maintenance of the MR systems.
  • Gary instructs new students and researchers in the nuances of MR imaging processes
  • Much of the MR control software and imaging pulse sequences depends on Gary's expertise and he is involved to the extent necessary to maintain a level of excellence in the images produced
  • Paramount to the imaging process are high-quality RF transceiver coils, and most of our coils have been designed and fabricated by Gary
  • Since monitoring of the animals is directly linked to the imaging process, Gary interacts significantly with physiologic monitoring systems to coordinate ventilation and heartbeat to imaging.
 
   
JAMES COOK - Systems Programmer  
919 684-7672   james.cook@duke.edu  
With a strong background in computer science, James supports the Center's computers and software, analyzes imaging data, provides technical assistance, and runs some of our imaging equipment. He is instrumental in developing image analysis pipelines to address both internal CIVM needs, as well as needs of our external collaborators in strategies to share image data. . He has been intimately involved in the development of the automated tensor calculation and segmentation pipeline for the mouse brain, and in the process acquired extensive knowledge on the required software components, achieving successful installation on several computing platforms, including the high performance cluster.  
   
TAWYNNA GORDON- Financial Analyst tawynna
919 684-7755   tawynna.gordon@duke.edu

 

Tawynna is the grants and financial administrator for the Center. She prepares and maintains financial documents to submit to funding agencies, coordinates financial data analysis, handles procurement for both large equipment and research supplies, and keeps the lab running with lots of other responsibilities.
 
If you need to see someone in the Center, your first stop will probably be with Tawynna.
 
 
 
   
YI QI MD - Laboratory Research Analyst II
919 684-7858   yi.qi@duke.edu
 
Yi handles the biological support for all of our live animal studies, and her help is critical in these studies. She focuses on surgery and setup of small animals, as well as preparing specimens for our many imaging modalities.
 

 

Dr. Qi also manages animal lab supplies, develops support and maintenance protocols, and trains our students, fellows, and outside collaborators. She maintains our animal database and orders animals for all users, and oversees the DLAR personnel who support our animal isolation facility. In addition to these many tasks, she also develops our animal isolation, transport, and surgical protocols.
 
 
 
LUCY UPCHURCH - Computer Systems and Network Manager
919 684-7781  lucy.upchurch@duke.edu
 
 
 
Lucy has over 20 years of system/network administration experience. She manages and supports all CIVM IT activities including all of the Center's computers and software, providing technical assistance to users within and outside of our lab.
 
She maintains the CIVM imaging network, including the extensive collection of workstations, Cloud GRID Visualization Servers, high performance cluster server, CIVM website, the Oracle imaging database, and the Oracle specimen database.
 
 
 
NIAN WANG - Post-doctoral Research Associate, Sr. Nian
919 684-7653  nian.wang@duke.edu
 
 
 
Nian moved to the Center from the Brain Imaging and Analysis Center, and is now participating in CIVM's brain imaging studies and analysis.
 
 
 
 
 

GRADUATE STUDENTS

 
Our grad students from the departments of Biomedical Engineering, Medical Physics, Computer and Electrical Engineering, the Medical School, Medical Scientist Training Program, and Radiology Residents on research rotations, all contribute greatly to CIVM's success.
 
JEFFREY ASHTON - Medical Scientist Training Program /BME PhD candidate jeff  
jeffrey.ashton@dm.duke.edu
Jeff is part of the Medical Scientist Training Program, now working on the PhD part of the program on CT studies under the direction of Dr. Cristian Badea from CIVM and Dr. Jennifer West from BME. His research includes using gold nanoparticles for CT functional and molecular imaging
   
Jeff's research has resulted in these publications (PubMed)
   
 
ELIANNA BIER - Medical Physics PhD candidate elianna  
651 408-2360  elianna.bier@duke.edu
   
Elianna is a Medical Physics PhD student working with the hyperpolarized gas MRI team led by Dr. Bastiaan Driehuys.
   
   
   
   
       
NATALIE DELPRATT - Biomedical Engineering MS candidate Natalie  
natalie.delpratt@duke.edu  
   
Natalie is in the Biomedical Engineering Masters degree program, and at CIVM, she is being mentored by Drs. G. Allan Johnson and Alexandra Badea, helping with various aspects of brain studies.  
   
 
 
 
 
 
     
MU HE - Electrical and Computer Engineering PhD candidate Mu  
919 684-7884     mu.he@duke.edu
 
Mu is part of the hyperpolarized team under the direction of Dr. Bastiaan Driehuys. Her research focuses on developing robust post-processing workflow for hyperpolarized gas MR imaging. Since hyperpolarized gas MR imaging has enabled radiation-free imaging of pulmonary function regionally and non-invasively, her current work is to develop an image analysis toolkit that can enable pulmonary disease phenotyping.
 
PubMed link to Mu's publications.
 
 
 
   
MATTHEW HOLBROOK - Biomedical Engineering PhD candidate Holbrook  
919 684-7715     matthew.holbrook@duke.edu

 

 
Matt is in the Medical Imaging Training Program in Biomedical Engineering and is working under the direction of Dr. Cristian Badea in researching the uses of spectral CT imaging in material decomposition and pathological diagnosis.
 
 
 
   
ROHAN VIRGINCAR- Biomedical Engineering PhD candidate rohan  
919 536-2214   rohan.virgincar@duke.edu

 

 
Rohan works with the hyperpolarized gas MRI team led by Dr. Bastiaan Driehuys. 129Xe has the unique property that it interacts with biological media in vivo, and in this process exhibits chemical shifts sensitive to the local tissue microenvironment.
Rohan's research involves understanding and characterizing these subtle signal changes, as well as extending 129Xe MR imaging and spectroscopy to different mouse models of disease to identify early signatures of disease onset and progression.
PubMed link to Rohan's publications.
   
     
ZIYI WANG - Biomedical Engineering PhD candidate Ziyi  
919 684-7884  919 808-6264  ziyi.wang@duke.edu
   
Ziyi is a Medical Imaging Training Program student and a member of the hyperpolarized gas MRI team, under direction of Dr. Bastiaan Driehuys. Ziyi helps the team best utilize 129Xe gas MRI in healthy and idiopathic pulmonary fibrosis patients.
   
   
 

GRADUATES and NEW POSITIONS

     
EVAN CALABRESE PhD MD evan  
evan.calabrese@dm.duke.edu
PhD Biomedical Engineering - 2014, MD 2015 Medical Scientist Training Program
Evan was in the Medical Scientist Training Program, which leads to both MD and PhD degrees. He completed his PhD part of the program in 2014, was a Post-doctoral Associate in CIVM for a year, and in 2016 finished Medical School for his MD degree. Evan's PhD dissertation was "Diffusion Tensor Imaging Biomarkers of Brain Development and Disease" and his contributions at CIVM resulted in many publications. Evan is now an MD Resident at UC-San Francisco.
See Evan's many publications at this PubMed link
     
KYLE DECKER MS kyle
MS - Biomedical Engineering, 2016
Kyle worked with the MR team under direction of Drs. Chunlei Liu and G. Allan Johnson.
 
 
 
 
   
RUSSELL DIBB PhD Russ
PhD - Biomedical Engineering, 2016
IAs part of the MR team under the direction of Drs. Chunlei Liu and G. Allan Johnson, in 2016, Russ defended his BME PhD dissertation "Probing Tissue Microstructure Using Susceptibility Contrast Magnetic Resonance Imaging." He is now back home in Utah working as an Image Quality Scientist at GE Healthcare.
 
PubMed link to Russ' publications.
   
MATTHEW FREEMAN PhD Matt
PhD - Medical Physics, March 2014
Matt was part of the hyperpolarized team under the direction of Dr. Bastiaan Driehuys. In 2015, he defended his dissertation on "The Efficiency Limits of Spin Exchange Optical Pumping Methods of 129Xe Hyperpolarization: Implications for In Vivo MRI Applications." Matt now works as a post-doctoral Research Fellow, Center for Pulmonary Imaging Research, Cincinnati Children’s Hospital.
PubMed link to Matt's publications.
 
 
S. SIVARAM KAUSHIK PhD  
PhD - Biomedical Engineering, Nov 2014
Shiv contributed greatly to the work of the MR hyperpolarized gases team. Shiv defended his dissertation in November 2014 on "Simultaneous Imaging of Hyperpolarized 129Xe Ventilation and Gas Exchange for Early Detection of Interstitial Lung Disease" and continued on in the lab as a Post-doctoral Associate. Shiv is now an MR Scientist, Applications and Workflow at GE Healthcare in Wisconsin. He can be contacted through gmail.
PubMed link for Shiv's publications.
 
     
SCOTT HAILE ROBERTSON PhD Scott  
PhD - Medical Physics 2016  
Scott was part of the hyperpolarized team under direction of Dr. Bastiaan Driehuys. A focus of his research was to optimize image quality in functional pulmonary MRI applications involving hyperpolarized gases. A goal of Scott's research was to exploit redundancy in undersampled k-space data to allow for the efficient acquisition of high-resolution multi-spectral images within a breath hold. Scott has stayed on at Duke University Medical Center for his post-doctoral studies in Clinical Imaging Physics - Quality Contractor.  
PubMed link to Scott's publications.
   
 
   
MENGHENG TOUCH MS meng  
MS - Medical Physics, 2016
Heng worked with Dr. Cristian Badea as part of the micro-CT team on research involving imaging processing and reconstruction algorithms for x-ray CT using a photon counting detector (spectral CT). He also worked on simulation of the spectral CT system for image reconstruction with material identification capability using non-linear optimization algorithms and exploring neural network algorithms. He now works as a Business Consultant at Applied Predictive Technologies in San Francisco. Heng presented his work at SPIE meetings and has a published paper: M Touch, DP Clark, W Barber, CT Badea, A neural network-based method for spectral distortion correction in photon counting x-ray CT Phys. Med. Biol. 61(16): 6132–6153, 2016.
     
LUKE XIE PhD Luke  
PhD - Biomedical Engineering, June 2014  
As part of the MR team under the direction of Dr. G. Allan Johnson, Luke's studies involved identifying age-related nephropathy in Sprague-Dawley rats using magnetic resonance histology. In 2014, Luke defended his dissertation on "Magnetic Resonance Imaging Biomarkers of Renal Structure and Function." He now works at Genentec and can be contacted through gmail.  
PubMed link to Luke's publications.
 


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