Bio-imaging/Molecular Imaging Research Overview
Bio-imaging/ Molecular Imaging
The field of Bio-imaging has experienced phenomenal growth within the last century. Whereas imaging was the prerogative of the defense and the space science communities in the past, with the advent of powerful, less-expensive computers, new and expanded imaging systems have found their way into the medical field. Systems range from those devoted to planar imaging using x-rays to technologies that are just emerging, such as virtual reality. Hardware design and software algorithm development for a wide array of imaging technologies applicable to medicine, including MRI, fMRI, PET and CT.
Faculty Research Interests
Bioengineering Building - Room 113
Summary : The research projects in our group are focused on the invention of new terahertz emission, detection and imaging technologies and their applications in biophotonics, medical imaging, non-destructive testing, material characterization and stand-off detection of chemicals. Our work spans electro-optic theory development, modeling, instrumentation and imaging signal processing techniques.
Laufer Center - Room 115C
Henry Laufer Endowed Associate Professor
Summary : The goal of my laboratory is to develop synthetic gene circuits (small constructs built from genes and their regulatory regions), and use them for biological discovery and practical applications (such as therapeutic gene expression control). For example, using synthetic gene circuits in yeast cells, we could demonstrate that noise (nongenetic cellular diversity) can aid microbial survival during antibiotic treatment and thereby enable the development of drug resistance. We have designed "linearizer" gene circuits in yeast cells that can tune a protein's level precisely, such that the protein concentration is proportional to an extracellular inducer and uniform within a cell population. We have moved this synthetic gene circuit into mammalian cells and can now tune the expression of a cancer-related genes precisely, to investigate how the level of tumor progression-related proteins affects invasion, migration and other metastasis-related cell behaviors. In the future, similar gene circuits may enable novel approaches to gene therapy. Our research is inherently interdisciplinary, since we use mathematical and computational models in combination with single-cell level measurements to characterize the dynamics of synthetic and natural gene networks, and to understand the cellular and multicellular behaviors they confer.
Health Sciences Tower
Professor & Vice Chair for Research
Summary : Benveniste's Laboratory focuses on (1) exploring, characterizing and understanding diagnostic MR contrast parameters suitable to visualize neuro-pathology in neurodegenerative diseases; (2) investigate transgenic animal models were specific genes are modified to understand mechanism(s) and treatment of addiction and of drug-induced neurotoxicity using high resolution MR imaging, (3) advance technologies in molecular MR imaging.
Health Sciences Tower 15-090
Summary : Despite major progress, cardiovascular diseases remain the leading cause of death in the western world. One of the major culprits in cardiovascular disease and in devices designed to treat or restore impaired cardiovascular function is the non-physiological flow pattern that enhances the hemostatic response mainly through platelet activation. Platelets have long been regarded as the preeminent cell involved in physiologic hemostasis and pathologic thrombosis. An innovative technique for measuring flow induced platelet activation has been developed, and its utility demonstrated in experiments conducted in recirculation devices (models of arterial stenosis, Left Ventricular Assist Device (LVAD), and mechanical heart valves). The mechanisms by which the non-physiologic flow patterns induce platelet activation and generate free emboli, that enhance the risk of cardioembolic stroke, was demonstrated in vivo with mechanical heart valves implanted in a sheep model. The results of this research will aid in elucidating physical forces that regulate cellular function in flowing blood, and may be applied to improve the design of blood recirculating devices and to develop more potent drugs for treating cardiovascular diseases.
Bioengineering Building - Room G05
Summary : Our goal is to better describe and understand the role of tissue heterogeneity in normal tissues and in the onset and development of diseases like cancer. Most tissues are comprised of a complex mixture of different cell types, and even cells within a clonal population exhibit a high degree of heterogeneity. However, the detailed behavior of individual cells is obscured in typical measurements which are averaged over cell populations. As a result, it has been difficult to comprehend the functional relevance of this heterogeneity due to the lack of adequate techniques. In order to enable the analysis of tissue heterogeneity we are developing an experimental approach based on droplet microfluidics that allows the manipulation of single cells by suspending them in drops carried in an inert fluid. These drops can then be automatically combined with reaction solutions, interrogated with fluorescent dyes or sorted to carry out sample preparation and analysis. My research exploits the advantages conferred by droplet microfluidics over conventional technologies and other microfluidics techniques in terms of automation, throughput and combinatorial power for the manipulation and analysis of single-cells.
Health Sciences Tower
Summary : Dr. Button's research work in the past has focused on Advanced Magnetic Resonance Mammography and Dynamic Infrared Imaging. His current research projects are infrared imaging, breast cancer detection, magnetic resonance and computer aided diagnosis (CAD).
Health Sciences Tower 10-020
Summary : Depression is a complex, heterogeneous disorder. It is most likely for this reason that neuroimaging has yet to uncover a clinically useful diagnostic or prognostic aid for people living with this disease, despite providing an unprecedented level of detail about the living human brain. As a biomedical engineers, we have the ability to incorporate the most current and technically advanced procedures in mathematics, image processing, and statistics in order to improve outcomes for patients diagnosed with Major Depressive Disorder (MDD) and other mental illnesses. My focus is to use advanced image processing algorithms to uncover the neurobiology of mental illness, and help improve both diagnosis and treatment. This includes: (1) developing algorithms to combine high dimensional multimodal data. Our group has a large repository of structural and functional Magnetic Resonance Images (MRI), Diffusion Tensor Images (DTI), and Positron Emission Tomography (PET) images of subjects with mental illness and controls. Fusing information from multiple modalities in a meaningful way may lead to personalized medicine options for those suffering from MDD and other illnesses; (2) Visualizing neurotransmitter systems in vivo. Examining neurotransmitter systems with PET can help us understand more about the pathophysiology of mental illness; and (3) Extracting the most accurate quantitative information from brain images using improved imaging sequences such as Diffusion Spectrum Imaging (DSI) and Arterial Spin Labeling (ASL). These high resolution imaging sequences can help us get the most complete and accurate view of the brain. Through advanced imaging techniques and image processing algorithms, we can help improve the lives of those suffering with MDD and other disorders.
Stony Brook University Hospital
Summary : Dilmanian's main area of research has been experimental methods of radiation therapy with segmented beams. In particular, he has been applying arrays of parallel, thin planes of synchrotron x rays (microbeams) at the National Synchrotron Light Source (NSL), BNL, to spinal cord injury research, and arrays of parallel, thin planes of carbon ion beams at the NASA Space Radiation Laboratory (NSRL), BNL, to cancer research in a geometry called interleaved carbon minibeams. Hi imaging projects have included computed tomography with beams of narrow energy bandwidth, and the use of microCT for body composition studies. Finally, he has been collaborating James Hainfeld, PhD and others on experimental methods of radiation therapy with dose-enhancing agents, such as gold nanoparticles.
Life Science Building - Room 002
Summary : The broad goal of this laboratory is to develop advanced optical instrumentation to detect and characterize physiological processes in living biological systems such as brain and heart. More specifically, cutting-edge optical spectroscopy and imaging techniques are developed that permit simultaneous detection of cerebral blood flow, blood volume and tissue oxygenation, as well as intracellular calcium in vivo. We are interested in studying drug-induced abnormalities of the brain function. Cocaine is chosen as one of the preliminary drugs for our research applications because it affects cerebral hemodynamcs, metabolism, and neuronal activities in the brain. The mechanisms that underlie cocaine's neurotoxic effects are not fully understood, partially due to the technical limitations of current neuroimaging techniques to differentiate cerebrovascular from neuronal effects at sufficiently high temporal and spatial resolutions. To solve this problem, we have developed a multimodal imaging platform that combines multi-wavelength laser speckle imaging, optical coherence tomography, and calcium fluorescence imaging to enable simultaneous detection of cortical hemodynamics, cerebral metabolism, and neuronal activities of animal brain in vivo, as well as its integration with microprobes for imaging neuronal function in deep brain regions in vivo. Promising results of in vivo animal brain functional studies demonstrate the potential of this novel multimodality approach to compliment other neuroimaging modalities (e.g., PET, fMRI) for investigating brain functional changes such as those induced by drugs of abuse.
Professor, Vice Chair for Research
Summary : Our group consists MR physicists, MR engineers, image scientists and application scientists, working collaboratively to advance MRI technologies and their biomedical applications. Our primary research interests are: (1) Development of in-vivo MRI and optical imaging technologies for studying the brain and the retina, (2) Application of imaging technologies to study normal anatomy, physiology and function in animal models and humans, and (3) Application of imaging technologies to study stroke, retinal degeneration and retinopathy in animal models and humans.
Summary : Developing a thin, flexible, fiber optic device based on Diffuse Correlation Spectroscopy (DCS) and Diffuse Optical Spectroscopy (DOS) principles that allows for the immediate detection of changes in spinal cord blood flow and oxygenation, in real time.
Summary : A senior chemist at Brookhaven National Laboratory, she focuses on the biochemical effects of drugs, aging, and selected diseases on the brain. Fowler received a Jacob Javits Investigator Award in the Neurosciences, in 1986 and 1993; a Gustavus John Esselen Award for Chemistry in the Public Interest in 1988; Brookhaven Laboratory's R&D Award, in 1994; the Aebersold Award from the Society of Nuclear Medicine in 1997; and the Francis P. Garvan-John M. Olin Medal in 1998.
Bioengineering Building - Room G19
Associate Professor & Undergraduate Program Director
Summary : Our emerging understanding of oxygen delivery to the tissues is that the blood flow within the smallest arterioles is tightly organized within repeating networks across the tissue. Central to this new paradigm are the concepts of vascular communication between the beginning and end of the network (via gap junctions), and its relation to flow sensing by the vascular endothelium. Our work has shown that different types of microvascular flow patterns can be triggered by direct stimulation of the focal adhesions (alpha-v-beta-3 integrins, i.e., wound healing), compared to adenosine (i.e., metabolic change), compared to nitric oxide (i.e., inflammation), hence we can control the flow patterns. Among the goals of this work are in vitro construction of transplantable microvascular networks, using bionanotechnology to create the sturdy scaffolding, and verification of nanofabricated drug delivery units within the vasculature. To this end, equally important are mechanotransduction of the physical forces associated with flow change (i.e., wall shear stress), the pharmacologic signal transduction systems involved (which guide drug discovery and intervention), and the molecular basis for the committed step that ensures healthy flow delivery. Our work employs computational modeling of the fluid mechanics, the physiology of arteriolar network blood flow (in vivo and in vitro), and precise genomic manipulation of key proteins in healthy and vascular disease states.
Bioengineering Building - Room G15
Summary : The Jia lab is an interdisciplinary research group focused on the development of novel biophotonic technologies for understanding complex biological systems at the nano-meter scale. We develop and apply various optical, computational, molecular, electrical and nano methods, such as super-resolution fluorescence microscopy, aiming to provide solutions for challenges in biological and medical research.
Computer Sciences - 203G
Distinguished Professor & Chair
Summary : Arie Kaufman is the director of the Center of Visual Computing (CVC) and the director of the Cube project for volume visualization supported by the National Science Foundation, Department of Energy, Office of Naval Research, Hughes Aircraft Company, Hewlett-Packard Company, Silicon Graphics Company, Howard Hughes Medical Institute, and many others. His research interests include computer graphics and specifically computer graphics architectures, algorithms, and languages; visualization including volume visualization and scientific visualization; user interfaces; virtual reality; and multimedia. Kaufman is the editor-in-chief of the IEEE Transaction on Visualization and Computer Graphics. He has lectured widely and published numerous technical papers in these areas, including the IEEE tutorial book on Volume Visualization. He has been the papers chair and program cochair for Visualization 1990-1994 and the chairman of the IEEE CS Technical Committee on Computer Graphics.
Health Sciences Tower
Summary : Jerome Liang focuses his attention on the development of quantitative SPECT systems, 3D virtual endoscopy, and computer aided diagnosis. This work includes creating a quantitative SPECT imaging modality as a cost-effective means for patient diagnosis as well as developing a high resolution PET as a functional research imaging modality. Liang is also striving to create a virtual colonoscopy as a cost-effective procedure for colon screening and to construct an automatic method for brain-tissue segmentation for diagnosis of disorders. In addition, he plans to build various models, in terms of physics, mathematics, and statistics, to simulate the practical problems above and then to validate the models by experiments. Liang has published his findings in journals such as Magnetic Resonance Medicine.
Bioengineering Building - Room G09
Summary : Research in our lab focuses on the embedded systems and high performance computing technologies in biomedical applications. Research projects have covered a vast range from the wearable wireless infant monitor for the prevention of sudden infant death syndrome to ultrasound scanning imaging device for the assessment of bone properties. We adopted the latest technologies in embedded system design and established own platforms for the medical device prototyping to facilitate the transition of intellectual properties from bench side to bed side. We are capable of building miniaturized medical devices using microcontroller based design and integrating large sophisticated devices using off shelf components. We specialize in FPGA technology for our HPC research project because it offers the flexibility of hardware configuration that also benefits the data acquisition and control aspects in the projects.
Brookhaven National Lab
Summary : Lisa Miller is the Life and Environmental Sciences group leader at the NSLS. She is also spokesperson for Beamline U10B and X27A. Beamline U10B specializes in mid-infrared microspectroscopy of materials such as biological tissues, polymers, coated and corroded surfaces, soils, minerals, and plants. Beamline X27A specializes in x-ray fluorescence microprobe analysis of trace metals in similar materials. Lisa Miller's research focuses on the study of the chemical makeup of tissue in disease using high-resolution infrared and x-ray imaging at the NSLS. Her work has two primary research areas: (1) examination of the chemical composition of bone tissue in diseases such as osteoarthritis and osteoporosis, and (2) correlation of metal ion content and protein structure in brain tissue in protein-folding diseases such as Alzheimer's disease and scrapie.
Computer Sciences - 261
Summary : Klaus Mueller's areas of interest are medical, scientific and information visualization, visual analytics, medical imaging, computer graphics, virtual and augmented reality, and high-performance computing. He has pioneered the use of programmable commodity graphics hardware boards (GPUs) for the acceleration of a wide variety of computer tomographic (CT) reconstruction algorithms and medical physics phenomena. Applications include diagnostic imaging, radiotherapy, electron microscopy, ultrasound tomography for breast mammography, and others. In the visual analytics area he works on devising new high-dimensional data visualization frameworks and combining them with statistical pattern recognition and machine learning to create intuitive interactive analytical reasoning environments for medical professionals. He is also working towards a comprehensive visual data mining environment for neuroscientists, called BrainMiner, to enable a more targeted and experiential derivation of brain functional models from large collections of knowledge and data.
Bioengineering Building - Room 119
Summary : Dr. Mujica-Parodi is Director of the Laboratory for Computational Neurodiagnostics (LCNeuro). LCNeuro obtains neural signals non-invasively through imaging by functional MRI, near-infrared spectroscopy, and electroencephalography. The complexity or chaotic features of these neural time-series are then quantified using a variety of computational techniques adapted from physics, such as power spectrum scale invariance, detrended fluctuation analysis, Hurst and Lyaponov exponents, and approximate entropy. Deviations from the critical degree of chaos are used diagnostically in conjunction with classification algorithms, to identify risk for illness even before a system has degenerated sufficiently to show onset of symptoms. Application of graph theory and dynamic causal modeling permits identification of the circuit-wide basis for this dysregulation, which in turn is used for developing treatment targeted to these specific circuits.
Cold Spring Harbor Labs
Summary : One of the major barriers to progress in systems neuroscience has been the lack of assays to survey the whole brain at cellular level of resolution, either with respect to anatomy or function. The Osten lab has established several automated microscopy and bioinformatics methods for whole-brain analysis in the mouse. These methods allow us to study cell type-defined neuronal circuits in normal brain and in genetic models of neurodevelopmental and psychiatric disorders. These disorders are becoming increasingly well understood at the genetic level, but what has been lacking is a reproducible and robust means to locate the impact of the genetic lesions on specific brain regions or neuronal cell types.
Bioengineering Building - Room G17
Summary : 2D and 3D cross-sectional optical imaging of biological tissue at close to cellular resolution (e.g., 10um) and at depths of 1-3mm can have significant impacts on noninvasive or minimally invasive clinical diagnosis of tissue abnormalities, e.g., tumorigenesis. Laser scanning endoscopes, based on optical coherence tomography (OCT), have been developed and tested on a wide variety of tissues both ex vivo and in vivo. Encouraging results based on animal and human studies show that LSE can provide morphological details correlated well with excisional histology, suggesting its potential for optical biopsy or optically guided biopsy to reduced negative biopsies in clinical practice. Current research of Dr. Pan's lab is focused on early-stage epithelial cancer detection, diagnosis of cartilage injury and healing, and assessment of engineering tissue growth. In addition, Dr. Pan's lab studies skin dehydration, geriatric incontinence and laser/biochemical attack to the eye using OCT and light microscopy.
Health Sciences Tower
Professor and Chair
Summary : The Center for Understanding Biology using Imaging Technology (CUBIT), under the guidance of Dr. Ramin Parsey and Christine Delorenzo, uses state-of-the-art imaging modalities to investigate psychiatric and neurological disorders. The goal of the lab is to develop, refine and apply brain-imaging techniques including positron emission tomography/magnetic resonance imaging (PET/MRI) to understand the biological causes of neuropsychiatric disorders and to improve their diagnosis and treatment. Several areas of focus of the lab include: 1) identifying biomarkers for diagnosis and predictors of treatment; 2) developing methods and modeling for neuroimaging; 3) understanding the serotonin system, specifically serotonin 1A and serotonin transporter systems, in major depression, bipolar disorder other mood disorders, and suicide; and 4) developing novel radio tracers. Using PET/MRI, we can better understand the neurotransmission deficits in psychiatric and neurological disorders that may aid diagnosis, identification of biomarkers and treatment targets to facilitate treatment development and ultimately to assist in treatment selection for precision medicine. Dr. Parsey has already established links with scientists at Brookhaven National Laboratory and with other departments at Stony Brook and aims to work collaboratively.
Bioengineering Building - Room 215
Summary : Early diagnostic of osteoporosis allows for accurate prediction of fracture risk and effective options for early treatment of the bone disease. A new ultrasound technology, based on focused transmission and reception of the acoustic signal, has been developed by Dr. Qin and his team which represents the early stages of development of a unique diagnostic tool for the measure of both bone quantity (density) and quality (strength). These data show a strong correlation between non-invasive ultrasonic prediction and micro-CT determined bone mineral density (r>0.9), and significant correlation between ultrasound and bone stiffness (r>0.8). Considering the ease of use, the non-invasive, non-radiation based signal, and the accuracy of the device, this work opens an entirely new avenue for the early diagnosis of metabolic bone diseases.
Professor and Associate Director
Summary : The Simmerling lab at Stony Brook University carries out research in the area of computational structural biology. In particular, the lab focuses on understanding how dynamic structural changes are involved in the behavior of biomoleculs such as proteins and nucleic acids.
Bioengineering Building - Room 115
Summary : Our laboratory seeks to integrate advances in nanoscience and technology with the biological sciences and clinical medicine to achieve significant advances in simultaneous molecular diagnostics and therapeutics (theragnosis), drug delivery, and bioengineering. Towards these ends, our research interests involve a multidisciplinary approach for the development of functional (electronic, optical, magnetic, or structural) bionanosystems as contrast agents for molecular imaging, as carriers for drug delivery, and as structural scaffolds for tissue engineering. Our current projects capitalize on the unique properties of carbon nanobiomaterials to develop a) advanced contrast agents (CAs) for molecular magnetic resonance imaging (MRI), b) nanocomposites to improve the physical and biological (osteoconduction and osteoinduction) properties of polymer scaffolds for bone tissue engineering and c) non-viral vectors for gene transfection. We have exploited the potential of Gd-based carbon nanostructures: Gd@C60 metallofullerenes (gadofullerenes) and Gd@Ultrashort-tubes (gadonanotubes) as a new generation of advanced CAs for MRI and shown them to have efficacies up to 100 times greater than current clinical CAs. Our recent studies show that they are particularly well suited for passive (magnetic labels for cellular MRI) and active (pH sensitive probes for cancer detection) MRI-based Molecular Imaging. Single-walled carbon nanotubes (SWNTs) have been proposed as the ideal foundation for the next generation of materials due to their excellent mechanical properties. We have dispersed SWNTs and ultra short SWNTs into fumarate-based polymers to form nanocomposite scaffolds that exhibit mechanical properties far superior to the polymers alone and are osteoconductive as well osteoinductive. Our research work involves material synthesis techniques, physico-chemical characterization techniques, tissue culture and in vivo studies.
Cold Spring Harbor Labs
Summary : Two challenges in cancer biology guide my work: first, how do tumors become addicted to certain gene products, and second, how do tumors develop resistance to anti-cancer drugs. I focus on the epidermal growth factor receptor (EGFR), which is both addictive when mutated and a common source of drug resistance.
Health Sciences Tower 4-141
Summary : Medical imaging techniques have undergone substantial growth in recent years, in both the research and clinical arenas. The standard anatomical imaging modalities of computed tomography (CT) and magnetic resonance imaging (MRI) have been complemented by quantitative functional approaches like positron emission tomography (PET) and single photon emission computed tomography (SPECT). Our lab develops new instrumentation and processing techniques not only to enhance the functional capabilities of PET, but also to combine it with synergistic modalities such as MRI to provide unprecedented, multidimensional information for cancer diagnosis, brain research, and many other applications. We have developed a miniaturized brain scanner for rodents (RatCAP) which avoids the potentially confounding effects of general anesthesia in rat brain studies, and even allows for the simultaneous study of behavior along with neurochemistry by PET. We have also developed new approaches for very high spatial resolution in PET, including a solid-state imager using cadmium zinc telluride (CZT) which achieves sub-mm resolution, and a monolithic scintillator detector with depth-encoding capability via a novel maximum likelihood positioning algorithm. And we have developed multiple imaging systems for simultaneous imaging with PET and high-field MRI, including a rodent brain scanner, a whole-body rodent system, and a prototype clinical breast imager. The research encompasses the development of new detector materials and concepts, low-noise microelectronic signal processing, high-throughput data acquisition methods, Monte Carlo simulation, and new data processing techniques to optimize the extraction of quantitative information from the PET data.
NIH National Human Genome Research Institute
Summary : The Organic Acid Research Section (OARS) studies a group of inborn errors of metabolism, the hereditary methylmalonic acidemias (MMA), and disorders of intracellular cobalamin metabolism. What has remained both perplexing and challenging is the wide spectrum of clinical phenotypes presented by the patients and the generally untreatable nature of many of the complications they display, such as renal disease in patients with isolated MMA and progressive visual deterioration in those with cobalamin C (cblC) deficiency.
Health Sciences Tower 4-120
Summary : Wei Zhao's main research interest is in the development of novel detector concept and new clinical applications for early detection of cancer. Her current research projects include (1) the characterization and optimization of a high-resolution flat-panel detector for digital mammography (imaging of the breast) through prototype development, image analysis, and computer modeling; (2) the development of detector technology and imaging system for three-dimensional imaging of the breast, which is aimed at achieving better detection of abnormality than existing two dimensional projection images; and (3) feasibility investigation of a large area flat-panel detector with amplification at each pixel for very low dose x-ray imaging applications.