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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

DIRECTOR - G. Allan Johnson PhD

Charles E. Putman University Professor of Radiology; Professor of Biomedical Engineering and Physics
919 684-7754
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). Our shared data provide access to other data sets.
MyBibliography link to publications.


ALEXANDRA BADEA PhD - Assistant Professor - Radiology
919 684-7654
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.
Link to Alex's publications, and Duke web page
CRISTIAN BADEA PhD - Associate Professor - Radiology, Biomedical Engineering, Medical Physics
919 684-7509
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.
MyBibliography for Cristian's publications, and his Duke web page
BASTIAAN DRIEHUYS PhD - Professor - Radiology, Biomedical Engineering, Medical Physics
919 684-7786
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.
MyBibliography link to Bas' publications.
LAURENCE HEDLUND PhD - Professor Emeritus of Radiology
919 684-7767
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
919 684-7769
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
PubMed link to John's publications.

FACULTY at other locations

CHUNLEI LIU PhD - Associate Professor of Radiology, Medical Physics, Biomedical Engineering
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
MARTIN FISCHER PhD - Associate Research Professor of Chemistry


TATIANA ALEXANDER - Administrative Assistant tatiana
919 684-7877



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
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.
He 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.
BJ presented this poster at the October 2015 Society for Neuroscience conference: RJ Anderson, JJ Cook, JC Nouls, M Foster, G Johnson, A Badea, A voxel-based morphometry pipeline in a computer cluster environment
DARIN CLARK PhD- Post-doctoral Associate Darin
919 684-7507
Darin defended his dissertation on "An Integrated Framework for Spectral and Temporal X-ray CT " in November 2015, and is staying on as a Post-doctoral Associate to continue his work under the 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 will continue to contribute to many of our CT technological advances and collaborations, and resulting publications. See this PubMed link.
GARY COFER - MR Operations Manager gary
919 684-7677

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 - Computer Programmer  
919 684-7672  
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.  
TAWYNNA GORDON- Financial Analyst tawynna
919 684-7755


Tawynna is the grants and financial administrator for the Center. She prepares and maintains the 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.
STACEY PRATT- Administrative Asisstant stacey
919 632-1426
Stacey joined CIVM to help with various administrative and financial tasks.


GEOFFRY SCHRANK PhD - Post-doctoral Research Scientist Geoff
919 684-7793
Geoff joined the hyperpolarization team from the Physics Department at the University of Utah. He brings experience in designing experiments and equipment to determine the existence and characterization of contaminants in Xe polarizers.


Under direction of Dr. Bastiaan Driehuys, he oversees the operations, maintenance, and continued development of CIVM's 129Xe hyperpolarization infrastructure in both a preclinical and clinical setting.
YI QI MD - Laboratory Research Analyst II
919 684-7858
Yi is responsible for 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 all our animal isolation, transport, and surgical protocols.
LUCY UPCHURCH - Computer Systems and Network Manager
919 684-7781
Lucy has over 20 years of system/network administration experience, and manages all CIVM IT activities.


She maintains the CIVM imaging network, including the extensive collection of workstations, Cloud GRID, the Oracle imaging database, and Oracle specimen database.
SALLY ZIMNEY - Educational Coordinator sallyz
919 684-7758
Sally has experience in technical and marketing writing, editing, graphics, and instructional design. She uses these skills to enhance all forms of communications, journal articles, grants, and reports that deal with the Center and the activities of the people who work here.
Sally is the contact person to initiate and schedule projects with CIVM. She also interfaces with long- and short-term visitors to the Center, and handles aspects of our training and educational activities. She also assists with IACUC activites to ensure that CIVM meets all regulations for animal studies.



Our graduate 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 the work of the Center.

JEFFREY ASHTON - Med Scientist Training Program /Biomedical Engineering PhD candidate jeff
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 is a 2nd-year Medical Physics PhD student working with the hyperpolarized gas MRI team led by Dr. Bastiaan Driehuys.
KYLE DECKER - Biomedical Engineering PhD candidate kyle  
919 684-7887
Kyle is in the Biomedical Engineering Medical Imaging Training Program and is part of the MR team under the direction of Drs. Chunlei Liu and GA Johnson for studies relating to susceptibility tensor imaging.
NATALIE DELPRATT - Biomedical Engineering MS candidate  
Natalie is finishing up her 1st year in the Biomedical Engineering Masters degree program under Dr. Kathryn Nightingale. At CIVM, she is being mentored by Drs. G. Allan Johnson and Alexandra Badea and is helping with a brain study.
RUSSELL DIBB - Biomedical Engineering PhD candidate Russ  
919 684-7839
As part of the MR team under the direction of Drs. Chunlei Liu and G. Allan Johnson, Russ exploits the usefulness of signal phase information acquired from gradient echo MRI of the brain.
Using a multi-echo sequence, Russ acquires gradient echo image volumes at multiple time points within a single scan, then employs mathematical tools to transform that data into enhanced magnitude, phase, and susceptibility images with reduced noise.
4D datasets also allow him to investigate T2* in the adult mouse brain, as well as the effect of magnetic field strength and contrast agent concentration on the susceptibility of brain tissues.
PubMed link to Russ' publications.
MU HE - Electrical and Computer Engineering PhD candidate Mu  
919 684-7884
Mu is part of the hyperpolarized team under the direction of Dr. Bastiaan Driehuys, and 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 image analysis toolkit that can enable pulmonary disease phenotyping.
PubMed link to Mu's publications.  
SCOTT HAILE ROBERTSON- Medical Physics PhD candidate Scott
919 684-7621


Scott is part of the hyperpolarized team under the direction of Dr. Bastiaan Driehuys. A focus of his research is optimizing image quality in functional pulmonary MRI applications involving hyperpolarized gases. Prioritizing spatial frequency information is imperative to optimizing the image information obtained by each RF pulse. A goal of Scott's research is to exploit redundancy in undersampled k-space data to allow for the efficient acquisition of high-resolution multi-spectral images within a breath hold.
PubMed link to Scott's publications.
MENGHENG TOUCH - Medical Physics PhD candidate meng  
919 536-2214
Meng works under the direction of Dr. Cristian Badea as part of the micro-CT team. His research involves imaging processing and reconstruction algorithms for x-ray CT using our photon counting detector (spectral CT). He also works on simulation of the spectral CT system for image reconstruction with material identification capability using non-linear optimization algorithms and exploring neural network algorithms.
ROHAN VIRGINCAR- Biomedical Engineering PhD candidate rohan  
919 536-2214


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 is a Medical Imaging Training Program student who is 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.


Some undergraduates work at CIVM part-time between their regular studies

  • NEIL DELWADIA (Brain segmentation)
  • CHRISTOPHER FLOWER (Physics, hyperpolarized gases)
  • CANYON DELL'OMO (Brain segmentation)


CIVM faculty work also with undergrads who are interested in small animal imaging on their honors theses projects and independent studies

  • SYED ADIL - Sr, Neuroscience major, honors thesis
  • KARISHMA POPLI - Sr, double-major Neuroscience / Global Health, honors thesis
  • LINDSEY KUOHN - Sophomore, Arts and Sciences
  • MICHELLE WANG - Sophomore, Electrical and Computer Engineering major




Matthew Langman MD, MSIS Christopher Long, MD, PhD Nancy Pham MD Lukas Ebner MD (Switzerland) Jennifer Wang
langman long pham lukas JenWang
MR renal studies Analyzing brain DTI data Analyzing canine brain data Cardiothoracic imaging, MR hyperpolarized gases MR hyperpolarized gases


PhD Biomedical Engineering - April 2014, MD 2015, Medical Scientist Training Program
MD candidate 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 has recently 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. See this PubMed link that includes an Open Access article and another that generated a Duke press release.
PhD - Medical Physics, March 2014
Matt was part of the hyperpolarized team under the direction of Dr. Bastiaan Driehuys. In March 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 Postdoctoral Fellow, Agnew National Security, Los Alamos National Laboratory, NM.
PubMed link to Matt's publications.
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 a Research Scientist at the Medical College of Wisconsin in Milwaukee, and can be reached through gmail.
See PubMed link for his publications.
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 as a Research Associate in Radiology Research, University of Utah. You can reach him through gmail.
PubMed link to Luke's publications.




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