There are considerable imaging resources available to the 55 faculty who are participating in this training program.  Where those resources are available to the whole community, we have summarized them under departmental resources.  In particular, immediately below we summarize the resources available in the Department of Radiology (Program Co-Director Jon Lewin is Department Director of Radiology at Johns Hopkins Medicine, Program Director Elliot McVeigh has been a faculty member of Radiology since 1988.)



(in order to simplify, we have grouped all of the Radiology Department and faculty resources together)


Overview of Research Space:

The Department of Radiology and Radiological Science currently includes approximately 43,500 square feet of non-office research space, including shared imaging facilities, animal surgery suites, wet lab, hot and cold chemistry, computational lab, and instrumentation development lab space.  In addition, approximately 40,000 square feet of trainee, post-doc, faculty, and staff offices are present within the department.


Overview of Major Equipment:

The imaging research infrastructure includes four research PET scanners (the GE Advance and the new brain dedicated HRRT (High Resolution Research Tomograph) of which there are only some 15 in the world and two GE PET-CTs. There are currently four dedicated research whole body MR imaging and spectroscopy systems (two 1.5 T and two 3T) at the Johns Hopkins School of Medicine.  In addition, there are also two research 3T MR systems at the Kirby fMRI Center, located on the Hopkins medical campus and funded in large part by an NCRR Research Resources Grant.  While directed and operated by Hopkins Radiology faculty, the Kirby Center sits at the center of a large multidisciplinary functional MR initiative that involves faculty from many departments across three institutions.  Installation of a whole body 7T scanner is now underway and should be complete by June, 2009.  With regard to animal imaging/spectroscopy and high-resolution MR microscopy, there are currently 4 instruments in the Department of Radiology spanning from 4.7 to 11.7 T and suitable for experiments with cats/rabbits through ex-vivo specimens.  In particular, a recently installed 9.4 T system for mice/rats has been constructed within our mouse barrier facility and is central to the institution’s transgenic mouse oncology and molecular imaging programs.  There is one 16-slice SPECT/CT dedicated for research along with substantial time available for research on a 64 slice CT scanner, as well as other whole body CT scanners.  There is a major molecular imaging center funded by P50 and SAIRP (Small Animal Imaging Resource Program) both funded by NCI. In addition to the MR systems noted above, this includes two small animal mouse PET scanners, a SPECT CT system, optical fluorescence/luminescence instrumentation, and confocal microscopy, all dedicated to in-vivo small animal imaging and spectroscopy. The molecular imaging program also has state-of-the-art molecular biology lab instrumentation. There is a state-of-the-art cyclotron producing 18F FDG for clinical PET as well as most significantly 11C or 18F research radiotracers available for some 20 to 25 PET slots per week, a record which is unmatched by most Research PET Centers throughout the world. There is a growing optical imaging group as well as research in ultrasound and tomographic physics. There is a dedicated large animal cardiovascular and oncological interventional research area that includes two digital subtraction angiography suites, an animal prep area, and a surgery room.  These systems include a Toshiba I series that is linked to a Vitrea 3-D reconstruction workstation, and a Philips flat-panel angiography system with rotational CT capability.  All procedure rooms are equipped with gas anesthesia machines, physiological monitoring equipment, and defibrillators.


The Department of Radiology at the adjoining Johns Hopkins Hospital currently has 8 CT scanners in place or under installation.  This includes one state of the art dual-source 64-slice CT (330 milliseconds per gantry/scan rotation), four single-source 64-slice CT, and three 16-slice multiple-row detector CT systems from various manufacturers.   A dedicated 40-slice interventional CT is also under installation.  In addition to the state of the art CT scanners, the division of body CT has a dedicated 3D imaging lab (under the direction of Dr. Fishman) that performs more than 2500 3D CT cases out of the total of 35,000 body CT examinations per year.


Phantom, volunteer, and patient studies will be performed in the clinics at the Johns Hopkins Medical Institution (JHMI).  Depending on the trainees project and mentor, these clinics can be in Radiology, Cardiology, Surgery, Oncology etc.  Hopkins Medicine staff are completely comfortable with performing additional procedures in compliance with approved research protocols.  The basic research facilities at JHMI occupy research space in the Johns Hopkins Hospital, the Ross Research Building, Traylor Research Building, and the Broadway Research Building.  A new 1.6 million square foot hospital building will be opening in 2011.  Planning for over 50 procedure rooms, many of which will have integrated imaging capabilities, is ongoing.



In addition to the animal facilities within the Interventional Radiology Research Laboratory, an animal laboratory facility is located within the MR Research Facility.  This facility includes three rooms, as well as an acute animal surgery room.  The rooms are located approximately 15-50 feet from the MR scanners.  The surgery room is equipped with surgical table, lights, canine and rodent respirators, electrocautery, defbrillator, blood gas analyzer, a Gould 4-channel chart recorder with pressure, flow, and EKG modules, a LabView-equipped with EKG, noninvasive pressure cuff, invasive pressure transducer, and a temperature probe, an end-tidal COmonitor, a mobile fluoroscopy unit, and a water purification system.

The BRB/ICE facility houses 60,000 small animal (mice, rats) cages and is a designated barrier facility. All animal facilities are under the direct control and supervision of the Department of Comparative Medicine.  All grant proposals are reviewed by the Institution to ensure that animal housing is available as proposed.  This Institution adheres to the caging requirements of federal law 89-544, 91-579, and relevant PHS regulations.  The Johns Hopkins University is fully accredited by the American Association for Accreditation of Laboratory Animals.


Radiology: Medical Imaging Physics Division( Dr. Ben Tsui)


Small Animal Imaging:

A 400 sq ft barrier facility is currently dedicated to small animal PET imaging. We already have much of core facilities and equipment for animal PET and SPECT imaging in place including an NIH ATLAS small animal PET scanner (Advanced Technology Laboratory Animal Scanner) which is a ring-type, high sensitivity, dual-layer phoswich PET scanner intended for imaging small animals such as rats and mice. The ATLAS detector array consists of 18 detector modules arranged around a circle such that the face-to-face diameter of the ring is 11.8 cm. Each detector module is placed in time coincidence with the seven opposite modules to give an effective transverse field-of-view of approximately six-cm and an axial field-of-view of two-cm. Each detector module consists of a 9 × 9 array of chemically etched phoswich elements with 2.25-mm pitch. Each of these elements consists of a 2 mm × 2 mm × 7 mm crystal of LGSO optically glued end-on to a 2 mm × 2 mm × 8 mm crystal of GSO. The GSO end is, in turn, optically glued to a Hamamatsu R7600-C12 position sensitive photomultiplier tube (PSPMT). Each phoswich element is packed into a 9 × 9 white vinyl egg crate covered at the entrance end with Teflon tape to enhance reflection of scintillation light onto the PSPMT photocathode.


Computer:  The Division of Medical Imaging Physics (DMIP) has the following computer workstations that will be available for computation needs for the proposed training grant: (1) A Beowulf-class cluster of 59 rack mounted computers with dual processors ranging in speed from 800 MHz to 2.0 GHz. The systems run Linux and each has 15-80 GB disk and 256-512 MB (with 2 nodes having 2 Gb) of memory and is connected by a 100 Mb or 1 Gb Ethernet switch. (2) Four servers connected by 1 Gb ethernet to the cluster ethernet switch and by 100 MB ethernet to the external network These servers provide login, control, and data storage, archiving and backup service for the nodes in the cluster. The servers all have 2 processors with speeds ranging from 1-1.4 GHz, 512 MB to 1 GB memory, and a total of 5 TB of RAID-5 disk space. (3) A dual 700 MHz processor PC running Linux with 350 GB disk and 512 MB of memory. (4) Two dual Athlon MP Linux workstations with dual processors (1.4 and 1.6 GHz), 2 GB MB of RAM and a 60 GB disk drive in each. (6) A file server for data backup with dual 1 GHz CPUs, 2 GB memory, and 8 160GB hard disks. Also, the DMIP has (2) more than 15 (with each member having an assigned computer) Pentium II and III, and Athlon XP systems running Windows XP with speeds ranging from 400 MHZ – 3 GHz, memory from 128 MB-4 GB, 3 IBM ThinkPad (T-40 and X-30) laptop computers for document preparation. A number of CD-writers and 4.7 Gb DVD+RW drives, one DLT-8000 (40 GB), and two Ecrix VXA-1 (33GB) tape drives, and a number of removable disk drives are available for data archival and backup. The following postscript-base laser printers are available for printing documents: a Xante 3G 2400 dpi laser printer; Xerox N17 (1200 dpi); Xerox Phaser 4400 (1200 dpi), HP LaserJet 6MP.  Several color inkjet printers and scanners, and one Lexmark C750n laser color printer. An Elmo EDP-5100 XGA LCD projector is available for presentations.


Major Equipment in Medical Imaging Physics Division (Dr. Tsui):

            The DMIP owns a large number of phantoms and inserts purchased from Data Spectrum Corporation and RSD. These are available for use for phantom studies to validate the compensation methods and algorithms. The phantoms available and relevant to this work include the microSPECT phantoms from Data Spectrum Incorporated.

            The DMIP also maintains an extensive collection of commercial and custom software for image processing, analysis and reconstruction. Commercial packages available on DMIP computers include Matlab, IDL, Mathematica, Kaleidagraph, MS Office, Autocad, Endnote, and Mathtype. The DMIP maintains and has extensive experience in the use of several Monte Carlo simulation tools for radiation transport siulation. DMIP users regularly use and modify the SIMSET/PHG and SIMIND Monte Carlo (MC) codes for simulation of Nuclear Medicine and PET imaging. In addition, customized versions of MCNP (versions 4B2, 4C) are available for use in either alone or in conjunction with SIMSET/PHG for simulation of photon interactions in collimators. The MCNP and MCNPX (version 2.4) codes are also available for simulation of simulation of photon and electron transport, e.g., for dosimetry applicatioins.

            The DMIP uses, has developed and continues to refine several realistic mathematical phantoms. The Zubal phantom has been used, primarily for simulations in the brain. The MCAT and NCAT phantoms, developed by the group, are mathematical phantoms with realistic organ shapes and orientations. In particular, the NCAT phantom is based on images from the Visual Human Project, with addition of models for cardiac beating and respiratory motion obtained from cardiac MR and chest CT, respectively. The model has been extended to the lower torso and extensions into the extrimeties and head are planned. One advantage of the phantom is the ability to simply scale the size and shapes of the organs.  Based on this technology, we have also developed a digital mouse phantom based on MR microscopy images, 4D tagged gated MR images and 4D respiratory gated MR images of normal mice.

            The DMIP has develoeped and maintains an extensively collection of tools for quantitative imaging and reconstruction. These include both analytic and iterative reconstruction and compensation methods, primarly for SPECT and planar NM, but also with tools available for PET and CT reconstruction. For SPECT, available methods include well validated methods for attenuation, scatter, and detector response compensation. These also include tools for simultaneous dual isotope imaging.  For microCT, we have cone and fan beam analytical and iterative reconstruction.

            A number of custom and open source image processing, display, analysis and quantitation tools are also available.



In addition, there is ready access to an adjacent, well-equipped machine shop (in the Hospital), electronic shop (in the Traylor Research Building), mass spectrometry facility (in the  Biophysics part of the Medical School Building), 300 MHZ NMR facility (in the Biophysics  Department, School of Hygiene and Public Health),


MAJOR EQUIPMENT in Nuclear Medicine Labs:

Automated gamma spectrometer, microprocessor-controlled;

Automated liquid scintillation counter, microprocessor-controlled;

5-Inch well scintillation counter with dual channel analyzer;

8-Inch well scintillation counter with multichannel analyzer;

Three G-M counting systems;

Three single channel analyzer well scintillation counters;

Proportional counter;

Two dose calibrators;

Gamma camera with associated image display and analysis system;

Nuclear stethoscope;

Miscellaneous survey meters;

Two benchtop G-M monitors;

Five chemistry hoods, three radioisotope hoods, two radio-iodination hoods and hazard hoods;

80 MHZ nuclear magnetic resonance spectrometer with H-1, C-13, and F-19 probes and variable temperature capability;

Scanning UV/VIS spectrophotometer, microprocessor-controlled;

Infrared spectrophotometer;

Gas chromatograph with TCD, FID and EC detectors;

Five analytical and semi-preparative high performance liquid chromatographs with UV, RI and radiodetectors as well as automated integrating recorders;

One preparative high performance liquid chromatographs;

Radiochromatogram scanner;

Column, gel and paper chromatography equipment;

High and Low voltage electrophoresis apparatus;

Four top-loading and three analytical balances;

Five centrifuges;

Three standard incubators and one CO2 incubator;

Five pH meters;

Two water purification systems;

Three BACTEC units;

Eight refrigerators/freezers;


Glassware washing facility.

Microdialysis Lab

NIH ATLAS small animal PET scanner

Linux workstation for data acquisition

DELL PC for user-interface and data processing

Dose calibrator

G-M survey meter with end-window probe

Two cylindrical micro phantom and 1 hot insert

Portable Pb container

Stand-alone mobile floor lamp

Refrigerator to keep dead animals overnight

Scale to measure accurate weight of small animals

Standard L-block shield + interlocking lead brick cave

Cs-137 standard source

Na-22 point source

P50 Lab Equipment


Radiology: Molecular Imaging Labs (Dr. Bhujwalla): ( )


Laboratory: The In Vivo Cellular and Molecular Imaging Center (ICMIC) Program occupies 2500 sq. ft of laboratory space in the Traylor Research building ..  ICMIC members also have access to four scan rooms and adjoining facilities in the MRI Building.  Included in this space is a heart perfusion laboratory, a biochemistry laboratory, two MR Oncology laboratories equipped with tissue culture apparatus such as sterile laminar flow hoods, -80 freezers, and incubators, an ELISA reader and a molecular biology area, 3 spectrometer rooms, an electronics shop, a small machine shop, an acute surgical suite and a computer room.  The JHU ICMIC Program also has a small animal dissecting microscope (Olympus), two phase contrast inverted microscope (Zeiss) for tissue culture studies, an optical microscope (Olympus) for histological and immunohistochemical analysis of tissue sections.  A CCD camera (Sanyo, Ltd.) is attached to the Olympus microscope to image the histological sections for the 3D reconstruction studies.  The images are directly transmitted to a Macintosh computer which is linked to a dedicated oncological imaging Silicon Graphics Octane Computer through the network.  Two Nikon fluorescent microscopes for cell fluorescence imaging and for in vivo and intact tissue fluorescence imaging (x1 and x2 objective) equipped with digital cameras  were recently purchased for the ICMIC program to promote combined optical and MR imaging.  We also have an optical imaging system to detect green fluorescence protein expression in vivo, and a fibre optic probe (Oxylite) for measuring oxygen tensions.  A chamber for inducing hypoxia in cells was also recently purchased.



Other: We have recently set up a fully equipped molecular biology laboratory in our Molecular Imaging program which includes two RT-PCR system s as well as equipment to perform protein and mRNA assays.  We have a dedicated HPLC system, a cryostat for cutting frozen sections, and a plate reader for bioluminescence and fluorescence assays. 


Major Equipment: The BRB Molecular Imaging Center and Cancer Functional Imaging Resource is a service center directed by Dr. Bhujwalla in the Dept. of Radiology together with an Advisory Board. The center is housed behind a barrier facility in the Broadway Research Building. The service center currently has a state of the art Bruker Biospec in vivo NMR Spectrometer equipped with a 9.4T /21 cm Ultrashielded magnet.  This instrument is equipped with two completely broadband high power RF channels and two sets of high performance gradient sets: a 120 mm (i.d.) BGA12 set capable of 400 mT/m maximum gradient strength per channel used for most experiments and a BG6 gradient unit (60 mm i.d.) which can develop upto 950 mT/m gradient strength, reserved for experiments requiring even higher gradient performance characteristics.  The second set can be inserted into the BGA12 unit and the switch-over is practically effortless.  Several commercial and home-built RF probes of varying sizes and designs, including actively decoupled surface coils in combination with volume excitation, are also available on this instrument.  Two high resolution vertical bore Bruker Avance NMR spectrometers, a two RF channel 400 MHz wide bore and a three RF channel 500 MHz WB, with microimaging capabilities are available in the MR facility.  Both of these instruments are equipped with a large array of commercial probes for both high resolution and micro-imaging applications on solutions, perfused organs and cells, fixed tissue samples and small rodents such as mice.  A 4.7 T Bruker Biospec spectrometer equipped with two sets of shielded gradients (12cm Bruker BGA-12 and 26 cm GE AccustarTM) with a 40 cm bore magnet is available for animal studies. All these spectrometers are connected to each other and other computers via high speed ethernet.  Each of these spectrometers is equipped with PC based animal monitoring and synchronization units as well as gaseous anesthesia equipments. The magnetic resonance research facility also has two 1.5T and two 3T whole body MRI scanners, equipped with high performance shielded gradients and multinuclear spectroscopy capabilities, dedicated to research on large animals and human subjects. 

 The NMR biochemistry lab is equipped with a Gilford Response UV-VIS spectrophotometer, a Gilford Fluoro IV spectrofluorimeter and a Dupont Sorvall RC2B refrigerated superspeed centrifuge.  A YSI 2300 Stat glucose and lactate analyzer for automated analysis of serum and whole blood glucose is also available.

There is a fully equipped molecular biology laboratory within which includes two RT-PCR systems as well as equipment to perform protein and mRNA assays.  There is a dedicated HPLC system, a cryostat for cutting frozen sections, and a Victor plate reader for bioluminescence and fluorescence assays.  There also exists a Xenogen Bioluminescence system, a small animal PET imager, a Faxitron system, and irradiator, and an ultrasound imaging unit. ( )


Radiology: Magnetic Resonance Research Division:


Data analysis and computer facilities

The Johns Hopkins Medical Institutions has facilities and resources for the development of MRI pulse sequences, image analysis software, and data analysis currently located in the Johns Hopkins Hospital, Outpatient Center near the PI’s office.  These include computers from Silicon Graphics Inc (SGI) and Sun Microsystems, Inc (Sun), DELL and Apple computers which are all heavily used by researchers.  The workstations include simulators for Philips, Siemens, and GE MRI systems for pulse sequence development.  In addition to these workstations, the investigators have desktop computers such as Apple and Dell windows machines for word processing, data analysis, and preparing presentations.

            All of our computers and MRI scanners are attached to a common ethernet network.  This facilitates transfer of pulse sequences and MRI data, minimizing cycle time for developing MRI pulse sequences.  Software has been installed and developed to facilitate development and debugging, communication, image processing, and data analysis.  There exists at least 500 GB of disk storage distributed throughout these facilities.

            Dr. Paul Bottomley is the Director of the Division of MR Research which has about 26 full-time faculty, including two people dedicated to management of the computer facilities and data. Joe Gillen manages the computer resources, maintaining and improving operability of the workstations and network, developing software and algorithms, and assisting with technical problems that arise.  Yohannes Afework manages image data produced by the Division's other research programs.  Collaborators also have access to workstations located next to the research MRI scanners that are operated and maintained by the MRI Service Center which is managed by the Division of MR Research

            In addition, the Department of Radiology has a "Center for Biomedical Visualization" (CBMV), an open access computer facility for the development of visualization software for medical applications.  The Center is equipped with SGI computers to accommodate the development of extremely graphics-intensive applications and real time image processing.  This resource is available at a charge to department researchers.

Standard software resources are available (Microsoft office, MatLab, Mathematica, NIH image J, Adobe photoshop, IDL) plus FEKO electromagnetic method-of-moment software for computing field and losses in an around MRI detectors, plus via special research agreement, MRI scanner source code and pulse sequence development software from Philips, Siemens and GE.

Animal, electronics laboratories and shop facilities

            A fully equipped animal lab is located within the MRI Research Facility in the Houck basement adjacent to a GE 1.5T and Bruker 4.7 T MRI instruments.  The laboratory has a mobile X-ray fluoroscope, surgical table, anesthesia machines and monitoring equipment, and is managed and operated by Dara Kraitchman a licensed veterinarian and faculty of the Division of MR Research, Dept of Radiology. 

            An electronics shop, located behind the animal laboratory, has a variety of equipment and space for testing, building, and repairing MRI coils (350 MHz Tektronix oscilloscope, Wavetek Frequency Generator, an old frequency synthesizer, drills, soldering equipment etc, a HP network analyzer, an RF noise meter, etc) and is available full time.  The facility is also overseen by the MRI Service Center and includes a partially-supported MSE Electronics Engineer who has RF MRI experience, with electronic testing and detector fabrication. A 2nd electronics shop has just been installed on the 3rd floor of the Park building adacent to the student/Fellow space (see below).


MRI facilities

            As of Feb ’08, the Department of Radiology has seven clinical MRI scanners: four Siemens (2 1.5T and two 3T) in our inpatient facility and a Philips  3T, a Philips 1.5T and a GE 1.5 T system located in the Johns Hopkins Outpatient Center.  The University’s MRI Service Center is directed by Dr. Bottomley, is in the Division of MR Research in the Department of Radiology, and operates four additional MRI scanners for research.  The MRI Service Center leases one scanner back to the hospital for clinical use, leaving 3 full-time scanners for 100% research use.  The scanners available are: {1} a GE 1.5T 8-channel Signa Horizon (50% research), {2} a Philips 16-channel 3T Achieva equipped with an X-ray C-arm (100% research); {3} a Siemens 3T Trio (100% research); and {4} a 1.5T Espree also equipped with a full angiographic floor-mounted X-ray fluoroscopic suite and miyabi table transfer system (50% research).  The scanners are supported by hourly machine rates, and have Radiology Technologist (RT) support by 3 RTs during normal working hours.  The RTs are also supported by the service center.

            In addition, the FM Kirby fMRI center in the basement of the Kennedy Krieger Institute over the road from the main hospital, also has two 100% research MRI scanners for use in the neurosciences.  These are {5} and {6} both Philips 3T scanners.  The FM Kirby Center is supported by an NIH P41 NCRR resource grant and is directed by Dr Peter van Zijl who is also in the Division of MR Research and heads the Neuroscience Section.  As with the MRI Service Center, the MRI instruments of the FM Kirby Center are available for research at hourly charges.  In addition, the Kirby center, with support from the Department of Radiology and other sources including the NIH has taken delivery of a new 7T Philips whole body MRI system, and the operation of the this new unit is anticipated in early 2009.

The Division of MR Research also manages 2 smaller bore NMR/MRI Service Centers.  The NMR Service Center has 400 MHz and 500 MHz Bruker NMR spectrometers, and a Bruker 4.7T 40 cm-horizontal bore spectrometer/imager equipped with rapid-switching gradient coils.  The second Service Center is the Broadway Research Building Molecular Imaging Center is primarily geared to animal genetic models in a closed environment.  It has a Bruker horizontal bore 9.4T animal system, in addition to an eXplore Vista small animal PET scanner, a SPECT-CT system, an IVIS Xenogen 200 optical imaging system for mice and rats, a VisualSonics small animal ultrasound unit, and a Faxitron MX-20 specimen radiography system.




Cardiology: The Translational Cardiovascular Ultrasound Research Laboratory


The Translational Cardiovascular Ultrasound Research Laboratory (TCUL) is located on Carnegie 5 (administrative offices and patient rooms), Carnegie 2 (analysis rooms) and Ross 1044 (small animal imaging facility. The TCUL is involved in cardiac and vascular imaging for multiple clinical and animal studies. The TCUL is directed by Dr. Theodore Abraham and managed by Kimberly Chadwell (Manager) and Anne Capriotti (Lead Sonographer). It consists of 2 full time sonographers and one part-time sonographer. There are 2 patient scanning areas and 2 patient interview areas. Although it is possible to share machines between the clinical and research facilities there are 6 machines dedicated only to research use. These include 2 Philips 5500 machines, one GE Vivid 7 machine, one Vingmed System FiVe machine, one GE Logic machine and one Acuson Sequioa machine. The analysis area on Carnegie 2 consists of several commercial and custom analysis workstations with high capacity processors and hard drive space. The work stations include: GE EchoPAC (1), Philips Enconcert (1), TomTec 4 dimensional Cardiovision workstation (1). In addition there are 2 workstations with vascular image analysis software for automated and semi-automated measurements of intima-media thickness and brachial reactivity.


Sonographers are experienced in clinical, large and small animal imaging. Protocols performed in the TCUL include: transthoracic echocardiography, stress echocardiography (dobutamine or exercise); tissue Doppler-strain echocardiography, three/four-dimensional echocardiography, carotid artery imaging and brachial artery reactivity studies.


Large Animal Echocardiography:

We routinely image conscious or sedated large animals (dogs and pigs) using a dedicated Vivid 7 ultrasound machine (GE Healthcare Milwaukee WI) equipped with a standard transthoracic 3.5 MHz broadband transducer, a 1.9 MHz non imaging transducer, a 15 MHz linear transducer and a 10 MHz phased array transducer. All transducers are capable of B mode and tissue Doppler imaging. Three dimensional imaging is feasible using a Philips IE 33 machine equipped with an X-4 matrix transducer capable of B mode and full volume 3D imaging. 


Small Animal Imaging

 The Small Animal Echocardiography Resource is located in Ross 1044 and houses a Visual Sonics Vevo 770 ultrasound system. This system is equipped with a 25 MHz and a 35 MHz transducer that allows high resolution rat and mouse cardiac imaging. The system is capable of B mode, M mode and Doppler imaging including tissue Doppler and strain imaging. The GE system equipped with a 10S phased array transducer or the 15 MHz linear transducer are also capable of small animal imaging and offer additional features such as color flow Doppler and speckle tracking strain imaging. The small animal imaging suite has access to an isoflurane vaporizer system for anesthesia. There is also a rail-based stereotactic imaging platform that allows “hands-free” imaging with inbuilt EKG and temperature monitoring systems and has a clamp for securing inhalational anesthesia tubes. This equipment facilitates high throughput small animal ultrasound scanning.


Data Management:

Images can be stored to machine hard drive, CD or DVD or magneto-optical disks. Data are then archived to a secure 2 tera-byte served administered by the Medicine Network (MNET) with quadruple redundancy. The analysis rooms in Ross 1044 have network access to the server. There are 6 high capacity workstations with an average processor speed of 3.2 GHz (including 2 workstations with dual processors) and 2-4 GB memory each. All terminals have access to the web, color printers, generic and custom image analysis software (EchoPAC for GE, Q-lab for Philips and Syngo for Siemens systems), word processing programs and statistical analysis/graphics programs.


Cardiology: O’Rourke lab


The O’Rourke lab accupies approximately 2500 sq. ft. on the 10th floor of the Ross Research Building. Four fluorescence microscopes with patch-clamp capabilities are available. All  microscopes are capable of fluorometric recording via 2- or 3-channel photomultiplier tube assemblies. Several imaging modalities are available, including a low-noise 1300x1100 pixel, cooled CCD camera (Micro Max, Princeton Instruments) with a 5MHz readout rate, and a Biorad 1024 Multiphoton laser scanning fluorescence microscope.  The latter is capable of simultaneous conventional (with a Krypton-Argon continuous wave laser) and two-photon excitation (with a 10W Millenia X pumped-Tsunami Ti:Sa mode- locked laser) which can be used to uncage molecules or perturb metabolism with subcellular precision (~0.8mvolume) and to image deep into intact tissues (~400m deep). The P.I. directs the Biorad facility, which is available on a fee-for-service basis to all Hopkins investigators.  All imaging microscopes are also equipped with patch-clamp equipment for simultaneous electrophysiological recording. A PTI fluorometer with spectral scanning and time-resolved fluorescence capabilities is also available for isolated mitochondrial studies.


Cardiology: Halperin Laboratory

Two HP xw9300 2.6 GHz computers, with dual processors and NVIDIA quadro FX3450 high performance graphic cards are in the Dr. Halperin’s laboratory. These will be used for the Visualization Workstation for real-time control of the MR or CT scanner, and for real-time image processing. One will be located in the MRI or CT scanner room to be used during testing, and the other, identical computer will be kept in the software development area and used for developing the applications. There is a similar Gateway E6500 computer in the Dr. Halperin’s laboratory.

            A 400 square foot electronics/ mechanical/ catheter fabrication shop is part of the laboratory. The shop contains a wide variety of hand tools and soldering equipment. The electronic instruments present include a 150 MHz oscilloscope, 100 MHz signal generator, digital volt meter, and1 GHz digital counter.  There is an Itasca 100L coil winding machine in the PI’s laboratory that can wind precision, miniature (1mm x 1mm) coils using wire as small as 0.001” in diameter (52 gauge), that is critical for making prototypes of the coils for the RF filters and tip location sensors. There is also a Beahm Designs Model 220B Split Die Thermal Bonder in the PI’s laboratory for making FDA-quality welds in the catheter tubes, for joining the flexible, non-braided distal tubes to the more rigid, braided catheter body tubes. A more advanced Beahm Designs 420-B Axial Compression Bonder is also present in the Dr. Halperin’s Laboratory. This advanced device has axial compression capabilities, which optimizes welding of tubes with different numbers of lumens, as will be present in the catheters being developed. A Miyachi Unitek UB25 resistance welding system is in the laboratory. This is a precision welding system which applies computer controlled electrical pulses to the parts being welded. This system incorporates a Stereozoom microscope for precision alignment of parts and allows welding of copper wires to the gold electrodes, which is critical in catheter building. All of this equipment is available full time.

A 400 square foot, fully equipped animal facility is also part of the laboratory. The equipment present includes animal surgery tables, operating lights, surgical instruments, Harvard ventilator, Narcomed gas anesthesia machine, GE 9600 fluoroscopy system, Pruka 64 channel electrophysiology recording system, computer data acquisition system, defibrillator, and surgical instruments.

            A cart with clinical grade electrical isolation is present in the investigator's laboratory for acquiring electrical signals during MR imaging and for performing ablations during MR imaging. This cart has the custom filters and shielding described in the application for making them MR compatible, and has received IDE clearance from the FDA.


Cardiology: Lardo Laboratory

Dr. Lardo is the principal faculty member who directs the cardiac CT system which is a 320 slice Toshiba AquillionOne.  In Dr. Lardo’s image analysis lab there are (11)Dell computers,(2)Toshiba AquillionOne 320 Consoles,(2)Toshiba 64 consoles (2)Vitrea 2 cardiac workstations, Dell Poweredge server 10 TB. Software licenses includeToshiba Myoperfusion,GE CineTool,Diagnosoft HARP, ZIOsoft, CT & MRI Medis, MATLAB,Merge efilm, Webpax.




BME: Center for Imaging Science (CIS) (Director, Michael Miller)


Laboratory:  CIS laboratory facilities in Clark Hall include 1,545 sq. ft. of graphics and computing laboratory and 2,279 sq. ft. of student laboratory/office space. CIS is a member of the Biomedical Informatics Research Network (BIRN), an NIH initiative that fosters distributed collaborations in biomedical science by utilizing information technology innovations. BIRN involves a consortium of 15 universities and 22 research groups that participate in one or more of three test bed projects on brain imaging of human neurological disorders and associated animal models.

            Through the involvement with TeraGrid and BIRN, the internal network infrastructure is configured to take advantage of the university's Internet2 access point. Internet2 is a consortium being led by 206 universities working in partnership with industry and government to develop and deploy advanced network applications and technologies, accelerating the creation of tomorrow's Internet.


The Robotics facility in the Vision Lab at CIS has two ER-1 robots manufactured by Evolution Robotics. Each ER-1 robot can be equipped with a 1.7 GHz Intel Pentium M 1 GB RAM Windows XP-SP2-based computer controller. Communication with the robot is performed over an 802.11 wireless link. A C++ API is used for programming and controlling of the robot motion as well as reading the sensor inputs on the robot. The sensors are (1) one Remote Reality Net-Vision 360 para-catadioptric omni-directional camera and (2) two orientation-customizable IREZ VGA cameras. These allow for complete vision-based control of the robot as well as environment monitoring and control. The robots are battery operated and have a dual output 15V 1A battery each. The ER-1 API also has hearing, speech, networking, remote control, email, autonomous mobility and gripping capabilities. The Vision Lab has a 280 sq. ft. dedicated Robot Playground and a number of computers with networked access to the ER-1 computer for control and output.


Computer:  CIS requires extensive computational resources for visualization and large storage management. The visualization workstations are used to develop volume=rendering algorithms. CIS provides Gigabit Ethernet network infrastructure to the desktop to support high-end visualization and date transfers. CIS has an open computer lab with 20 high-end, graphic workstations that are available and used by visiting faculty and scholars, and graduate and undergraduate students. In addition, CIS has 50 high-end, graphic workstations dedicated to research and located in the offices of faculty, graduate students, research technicians and research programmers and three workstations used to support Center administration.


Office:  CIS has 1,686 sq. ft. of offices and 651 sq. ft. of conference room and administrative areas. This space combined with the laboratory space provides a total of 7,500 sq. ft.


Other: MAJOR EQUIPMENT:  The major computational machine within CIS is the Intel Itanium2 cluster. This machine is used for local development and the porting of applications to various National Supercomputer centers.  The Intel Itanium2 Cluster consists of 32 Itanium2 processors. Each dual processor node shares 4GB of memory (64GB total) and Gigabit or Myrnet network for high speed cluster communication. The cluster is used as a development machine for TeraGrid applications. The TeraGrid is a multi-year effort to build and deploy the world's largest, most comprehensive, distributed infrastructure for open scientific research. The TeraGrid includes over 20 teraflops of computing power distributed at nine sites, facilities capable of managing and storing over 1 petabyte of data, high-resolution visualization environments, and toolkits for grid computing. For large memory computational requirements, the CIS infrastructure provides two 32GB/8cpu and one 128GB/16cpu computational servers. All the components are tightly integrated and connected through a network that operates at 40 gigabits per second. The CIS internal infrastructure supports a gigabit network infrastructure to desktop; 120TB of data storage; three tape libraries with a backup capacity of over 210TB; and over 35 visualization workstations.

OTHER RESOURCES:   CIS is an interdisciplinary research center with a full-time director and 11 affiliated faculty members at the Whiting School of Engineering from Biomedical Engineering, Electrical and Computer Engineering, Applied Mathematics and Statistics, and Computer Science and from the School of Medicine.  In addition, the Center employs a research scientist; two post doctoral fellows, two research technicians, a research programmer, and 30 graduate students.  Support staff includes a Research Administrator, Manager of Computer and Network Systems, Software Engineer, Software Engineer and Administrative Coordinator.

BME: Biophotonics Research Laboratory (Director, Xingde Li)

All the equipment and other resources at the Biophotonics Research Laboratory in the Department of Biomedical Engineering will be available for use in the proposed training program.  These include lab and student office space, a wide range of commercial and home-made high-speed ultrahigh-resolution imaging and spectroscopy systems, software, nanomaterial synthesis and cell culture facilities.

Individual Equipments that are relevant to the translational training proposal and will be used for imaging and nanosynthesis include:

1.     General-purpose microscope (Zeiss Axivert 200): brightfield, darkfield, fluorescence (visible - NIR), phase contrast, DIC, polarization 

2.     Confocal microscope (Olympus)

3.     Multiphoton fluorescence microscope (home-built on a Olympus microscope base)

4.     Home-built high-speed (10-80 fps) ultrahigh-resolution (5-8µm) endoscopic OCT imaging systems at 800 nm and 1300 nm wavelengths (time-domain, spectral domain and swept source)

5.     Tunable femto second laser (680 – 1080 nm) (Coherent Vision)

6.     Tunable nano second laser (700 – 1000 nm, 1150 – 2400 nm) (Continuum)

7.     Home-built Kerr-lens mode-locked Ti:Sapphire laser (7-8 fs, small footprint 28 x 75 cm)

8.     Two cooled single molecule detection CCD cameras (front and back illuminated)

9.     Home-built small animal whole-body fluorescence tomography system (hardware and image reconstruction software)

10.  High-resolution imaging spectrometer

11.  High-speed data acquisition systems (200 Ms/sec)

12.  Near-infrared frequency-domain photon diffusion spectroscopy system for measuring tissue optical properties and physiological parameters (such as absorption, scattering, tissue oxygenation and hemodynamics etc)

13.  Fiber-optic scanning nonlinear endomicroscopy imaging system (two-photon imaging and second harmonic generation imaging)

14.  Two Optical Spectrum Analyzer (400 – 1750 nm)

15.  Fiber-optic Fusion Splicers (2), Cleavers (3) and Polisher

16.  Temperature-control nano synthesis station

17.  Temperature controlled centrifuge

18.  Cell Culture Incubators

BME: I-STAR Laboratory (Director Jeff Siewerdsen, (opening July 2009))

The Imaging for Surgery, Therapy, and Radiology (I-STAR) Lab. Dr. Siewerdsen heads the I-STAR laboratory located in the Traylor Building, comprising ~1200 sq. ft. of dedicated research space. The lab will contain a variety of resources for the development and rapid translation of new imaging technologies, including:

1. an x-ray imaging benchtop for cone-beam CT and other advanced x-ray modalities;

2. a prototype C-arm developed for cone-beam CT surgical guidance;

3. a Volume Image Visualization and Analysis (VIVA) lab to support preoperative surgical planning, performance evaluation, and human observer studies using advanced 3D image analysis tools;

4. a dedicated instrumentation bench for development of real-time tracking and surgical navigation systems;

5. basic machine shop and hardware development resources.

The I-STAR lab offers space appropriate to approximately 4 research associates and 10 students.

 The Minimally Invasive Surgery Training and Innovation Center (MISTIC). The MISTIC facility comprises ~6200 sq. ft. in the JHU Medical Center (Blalock Building) dedicated to surgical training, simulation, and preclinical (animal and cadaver) studies. In collaboration with Dr. Michael Marohn (Associate Professor of Surgery), Dr. Siewerdsen has access to a ~800 sq. ft. laboratory in MISTIC along with office space for 2 research associates. The MISTIC facility provides an ideal proving ground for the rapid translation of new technologies out of the laboratory and into clinical trials. The laboratory houses a prototype C-arm developed in collaboration with industry partners for intraoperative cone-beam CT along with novel systems for real-time tracking and navigation. The facility offers a fairly complete armamentarium of surgical instruments, tracking systems, anesthesia, and disposable equipment. The space incorporates multi-media teaching systems, bi-directional audio/video connections to ORs, endoscopy suites, auditoria throughout JHU, offices, a meeting room, instrument washers / disinfectors, two tissue preparation rooms, and cold storage facilities.

I-STAR Computing Resources. The I-STAR Lab includes ~15 computer workstations integrated with the BME network along with a dedicated server for data archiving (2.0 TB) and fast 3D image reconstruction (2.5 GHz quad-CPU). Computers include 3 acquisition / instrumentation workstations (Pentium-based PCs with 2GB RAM); 3 image analysis workstations (dual-Pentium PCs with 2 GB RAM); and ~9 general purpose workstations for data analysis. Workstations in the VIVA lab incorporate 4 diagnostic-quality medical displays (3-5 MP monochrome displays) along with advanced 3D image analysis and visualization software (MIMICS v11.1 for 3D visualization, segmentation, and finite-element analysis along with custom applications developed in open-source VTK, ITK, and IGSTK environments). Matlab (2008b), Origin, and statistical analysis software (SPS) are available on workstations throughout the laboratory.

I-STAR Specific Equipment Available to the TPTRI Program:

1. Research Prototype for C-Arm Cone-Beam CT. Dr. Siewerdsen worked in collaboration with industry partners to develop a cone-beam CT-capable, mobile, isocentric C-arm for guidance of interventional procedures. The system has been used extensively in laboratory, preclinical, and clinical studies of image-guided surgery and is available to the program, housed within the MISTIC facility at JHU Medical Center.

2. Experimental Benchtop for Cone-Beam CT: An experimental bench located in the I-STAR Lab provides a precise, flexible platform for investigation of imaging performance in flat-panel cone-beam CT and other advanced x-ray imaging modalities, such as tomosynthesis and dual-energy imaging. The bench features an 8-axis motion control system. The x-ray source is an 80 kW x-ray generator and Varian Sapphire Rad94 x-ray tube. The detector mount allows interchangeable detector configurations.

3. Instrumentation Benchtop: An experimental bench in the I-STAR Lab developed using Dr. Siewerdsen’s startup funds provides a flexible platform for investigation of novel tracking, robotics, and navigation systems in image-guided interventions. It is based on a precision, multi-axis motion control system designed to support integration of auxiliary instruments for image-guidance, including optical tracking systems (Polaris), electromagnetic tracking systems (Aurora), endoscopes, needle positioning systems, and robotics (to be implemented)


ECE: Image Analysis and Communications Laboratory (Director, Jerry Prince)

The Image Analysis and Communication Laboratory comprises 1,968 sq. ft. in Clark Hall, the main building for Biomedical Engineering on the Homewood Campus of the Johns Hopkins University. The laboratory space consists of 993 sq. ft. of office space used by faculty and staff.  The graduate students workspace and research laboratory area together consists of 975 sq. ft. of space.  IACL also has use of a shared server room with about 1200 sq. ft. of space.  The laboratory has several major pieces of equipment as listed below:

·        Two Intel Pentium based Machines each comprised of Dual 64 Bit Xeon processors running at 3.2 GHz, 8GB Ram, 16x DVD-DL Burner, 1920 by 1200 pixel monitors running RedHat Enterprise Linux.

·       Three Intel Pentium based machines with Eight 64 Bit Xeon processors running at either 2.9GHz or 3.7GHz, and between 16 and 32GB of Ram, with 16x DVD-DL burner.

·        Three Intel Pentium based Machines each furnished with Dual Xeon Processors running at 3.0 GHz, 4GB Ram, Dual Monitor Set Up with 3200 by 1200 desktop area, running Microsoft Windows 2000 and SuSE Professional Linux.

·        Two Intel Pentium based Machines each incorporating Dual Xeon processors running at 2.4 GHz, 3GB Ram, running Fedora Core Linux.

·        Two Intel Pentium based Machines each containing Dual Xeon processors running at 2.2 GHz, 4GB Ram, running Fedora Core Linux.

·       Four Disk Arrays providing more than 7 Terabytes of storage space while operating in RAID Five mode and potentially more than 8 Terabytes in a Non-RAID mode.

·       Linux cluster comprising nine 2.2GHz Pentium 4 nodes, each with 1.5GB RAM, running Fedora Core and Condor Clustering Management software.

·       Six Intel Pentium IV based machines running at 2.0-2.4 GHz, 1GB Ram, 1280 by 1024 desktop running Microsoft Windows 2000 and XP.

·       One Intel Xeon Dual Processor workstations 1.7Mhz, 1GB Ram, DVD/CD writer and 1280 by 1024 pixel color monitor.

All Linux Workstations include the following software:

·       Research: Matlab 7.0, LAPACK, LAM.

·       Visualization: OpenDX (formerly Data Explorer from IBM), MIPAV, Gimp, ImageMagick, Osiris.

·       Development: C Complier (GCC and ICC), GDB, DDD, Electric Fence, Memprof, Valgrind.

·       Productivity: CVS, Emacs, OpenOffice, LaTeX.

            All Windows Workstations include the following software:

·       Research: Matlab 7.0.

·       Visualization: MIPAV, Osiris.

·       Development: Microsoft Visual C++ and associated Visual Studio Tools, IDEA Java IDE.

·       Productivity: Microsoft Office, Microsoft PowerPoint, Corel Draw, CVSNT, Cygwin.

Apart from the above mentioned workstations, the lab has other peripheral equipment:

·       Hewlett Packard 8100 DN PostScript Laser printer.

·       Dell 5100CN Duplex Color Laser Printer.

·       IBM LTO Tape Backup Drive and autoloader, with 1.6 Terabyte capacity.

·       IBM LTO 3 Drive, the drive supports tapes with a capacity up to 800GB and is backward compatible with LTO versions 1 and 2.

·       Sharp Notevision LCD Projector.

·       Microtek 5950 Flatbed Scanner, supporting resolutions up to 4800x4800 dpi.


Comp Sci: CISST LABORATORY (Taylor, Hager)



CISST ERC: The CISST ERC facilities occupy approximately a 15,000 square foot  space in a new Computational Sciences building. This includes 6,000 square feet of laboratory space with individual labs for 9 robotics and vision faculty opening onto 2,500 square feet of shared lab space.  In addition to computers, desk space, bench space, etc., the lab space includes a small NC machine shop for prototyping and a large optical

bench for microsurgery and other experiments.  These labs are frequently used as engineering/system integration staging areas and equipment frequently migrates back between the Engineering School and experimental space at the Johns Hopkins University Hospital.  The building also has a 782 square foot “mock” operating room that will be available for system integration experiments.  We plan to add a da Vinci “S”

robotic surgery system to the “mock” operating room in the near future. CISST also has a 340 square feet experimental laboratory space in the Traylor building of the Johns Hopkins University Hospital complex, adjacent to a fully equipped large animal imaging and operating facility. This laboratory is often used as system

integration staging and rehearsal area for in-vivo human and animal trials. 


The Minimally Invasive Surgical Training Center (MISTC): 12th floor Johns Hopkins Hospital CMSC Building. Completed in 2001, this center comprises a 6200 sq ft facility consisting of two fully-equipped operating rooms and five preparatory/storage rooms.



The CISST laboratory has an extensive network of over 60 fast PC-based computers (5 are servers) for research and office use, together with printers and other data processing equipment and access to 5 SGI graphics computers and an ONYX infinite reality machine.  In addition, it has many specialized computer systems for control of experimental apparatus.  Dr. Okamura also has additional computing resources

including 8 networked PCs.



Offices for 9 robotics faculty as well as administrative and engineering staff and postdocs are located on the first floor of the Computational Sciences building. Student offices for approximately 50 graduate students are also located on the first floor.  



The CISST Lab also provides a small machine shop equipped with a CNC machine for small jobs.  More extensive facilities are available in the Mechanical Engineering.