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NeurotechEU-NEURICOO Match Making: NEUROFUND Capacity Building Sessions #3

Published on:

Advanced Medical Imaging Technologies

with short presentations

of several laboratories of Bogazici University:

“NeuroSignal Analysis Laboratory”

“Past and Current Research on Neuroimaging and Neurosciences at VAVlab”

“Precision Medicine Group Research Activities”

” Magnetic Resonance as a Central Station: Merging Various Disciplines”

“Physics and Disease”

“Research at XLAB: Democratization of Medical Imaging”
“Research at the Computational Imaging Laboratory”

23 November 2021 (Tuesday);   12.00 (!) – 14.00 


Ahmet Ademoğlu (BME), Burak Acar (EE), Albert Güveniş (BME),
Alpay Özcan (EE), Burçin Ünlü (PHYS), Cengizhan Öztürk (BME), Esin Öztürk Işık (BME)

Boğaziçi University


Zoom Meeting
https://boun-edu-tr.zoom.us/j/94970805819   (Passcode: 149556)


About The Seminar:

Medical imaging technologies have gained importance in understanding the human anatomy as well as its function and metabolism, and have shed light into the mechanisms of several diseases, including cancer, neurodegenerative disorders, and muscular diseases. This seminar will provide insight into several research projects conducted at the medical imaging laboratories of Boğaziçi University.

The order of the highlighted laboratory/project presentations will be as follows:


“NeuroSignal Analysis Laboratory”

Ahmet Ademoğlu, PhD (BME)


NeuroSignal Analysis Laboratory is focused on neuroimaging studies related to EEG Source Reconstruction, fMRI Data Processing, EEG-fMRI Multimodal Data Integration, Connectivity Analysis and Brain Computer Interfacing. Some fundamental results of former research projects conducted in collaboration with national and international institutions will be presented. The technical expertise and experience of the laboratory in EEG and fMRI processing will be described.


“Past and Current Research on Neuroimaging and Neurosciences at VAVlab”         

Burak Acar, PhD (EE)


Bogazici University, Electrical & Electroncis Eng. Dept., VAVlab group has been conducting research in signal and image processing and analysis with a primary focus in medical sciences. The topics range from data acquisition to post-processing and analysis, including mechine learning applications. This short presentation aims at providing an overview of our diverse set of research topics with emphasis on brain imaging and signal/image processing in neurosciences. The focus will be on diffusion imaging, tractography and structural-functional brain network analysis, among which the latter constitutes our primary current research interest.


“Precision Medicine Group Research Activities”

Albert Güveniş, PhD (BME)


In this brief talk we present the main activities of our group that aim to improve the precision of diagnosis and therapeutic interventions for individual patients. We use two approaches in our research. First, we use stochastic systems modeling and optimization techniques to enhance the diagnostic capability of medical imaging systems, in particular, molecular imaging systems such as PET and SPECT. Second, we use mathematical modeling and machine learning methods for characterizing diseases as well as predicting a therapy response for individual patients. Some of these techniques have been developed for applications in oncology. They are now being translated to neurology as therapeutic options become available for diseases such as Alzheimer’s Disease. We will give examples of our activities and achieved results.


“Magnetic Resonance as a Central Station: Merging Various Disciplines”

Alpay Özcan, PhD (EE)


Magnetic Resonance Imaging (MRI) is an extremely versatile tool that allows transdisciplinary collaborations including but not limited to systems science, mathematics, engineering, chemistry, physics, biology and medicine. As a demonstration of MR’s wide range of theoretical and applied scientific areas, in this talk we will quickly overview an MR compatible robotic device, optimization of diffusion tensor imaging data acquisition schemes, a new model for diffusion MR, quantitative susceptibility mapping, interactive feature space methodology for pathology detection in prostate cancer and application of machine learning for breast cancer and glioma.


“Physics and Disease”

Burçin Ünlü, PhD (PHYS)


I will discuss the relationship between physics and disease. I will also briefly talk about the imaging systems developed in our laboratory (photoacoustic microscopy, Raman spectroscopy, femtosecond lasers, etc.)


“Research at XLAB: Democratization of Medical Imaging”

Cengizhan Öztürk, PhD (BME)


Personal research experience will be presented first. The main theme is image guided therapy, ranging from interventional MRI, X-Ray Imaging fused with MRI and cardiac MRI. A brief introduction of the concept of “Democratization of Biomedical Technologies” will be given next. An overview of ongoing research at XLAB (https://xlab.boun.edu.tr/) will be presented as examples of this approach: a plug-integrate-play hardware components and an open software platform for a novel X-ray based medical imaging device.


 “Research at the Computational Imaging Laboratory

Esin Öztürk Işık, PhD (BME)


Computational Imaging Laboratory at Boğaziçi University works on developing novel magnetic resonance imaging techniques to allow for a better understanding of underlying disease mechanisms in patients with brain tumors and Parkinson’s disease with the overarching goal of translating this knowledge into clinical support tools to improve patient quality of life. The technical projects at the laboratory have focused on designing new algorithms for advanced MR imaging data acquisition, post-processing, quantitation and analysis. The laboratory has also worked on developing computational methods based on classical machine learning and deep learning for MR image analysis to understand disease mechanisms. In this talk, the results of the recently funded projects will be briefly discussed.


About the Speakers:

Ahmet Ademoğlu received his B.S. in Electrical & Electronics Engineering, his M.S. and Ph.D. degrees in Biomedical Engineering, all from Bogazici University, in 1987, 1990 and 1995, respectively. He worked as a postdoctoral fellow at Texas Medical School in Houston from 1995-1997. He has been working as a full time academic faculty in the Institute of Biomedical Engineering at Bogazici University since 1997. His research interests are neuroimaging and biomedical signal processing.

Burak Acar received his PhD in electrical and electronics engineering, from Bilkent University, Ankara, Turkey, in 2000, on Electrocardiogram (ECG) signal processing and analysis.  He worked at St. George’s Hospital Medical School, London, UK during his PhD and later joined (LUCAS MRSI Center) 3DQ Lab at Stanford Medical School, Dept. of Radiology, CA, USA, where he worked as a post-doctoral fellow on virtual colonoscopy and diffusion MRI brain imaging. He moved to Bogazici University in 2003, where he is currently a full professor at Electrical & Electronics Engineering Department. He was a Mercator Visiting Professor at TU Munich, Department of Informatics, Chair of Computer Aided Medical Procedures (CAMP), Munich, Germany, in 2012-2013. His research interests cover a diverse range of topics in the medical/biomedical domain, including medical decision support and CAD systems, biosensor data processing, search & retrieval, medical image simulations, ML on/of graphs (more specifically brain connectome analysis via fMRI/dMRI and applications to neurodegenerative diseases). He collaborates with national and international research groups, including Istanbul University (Capa) Medical School, Koc University, Stanford University, TU Munich, UIUC. His publications and US patents, received over 1800 citations (WoS). He is the recipient of the Excellence in Research Award from Bogazici University Foundation (2006), the Young Researcher Award from Turkish Academy of Sciences (2008).

Albert Güveniş

Education: Drexel University USA (MSc and PhD)

Faculty Positions: Drexel University, University of Pennsylvania, Inst of Biomedical Eng / Bogazici University

Member, IEEE, Drexel University Engineering Alumni Assoc, American Heart Association AHA, QIBA (RSNA)

Cooperated with major international institutions JCI, ECRI, WHO, EU for quality assurance and training programs in biomedical engineering

Technology development: Published US patent on a 3D model for apnea management, led to a successful start-up

Awards: Best paper award in Hungary, Tema award at IEEE conf, many invited speeches internationally

High impact publications and many expert reviews of articles in SCIE and other indexed journals
Work area: Computational methods for the precision detection, modeling and management of major diseases

Alpay Özcan received the B.S. degrees in Electrical and Electronics Engineering and Mathematics with honors from Boğaziçi University, the M.Sc. with distinction in Electrical Engineering from Imperial College, the M.S. and the D.Sc. degrees in Systems Science and Mathematics from Washington University in St. Louis. Subsequently, he joined the Biomedical MR Laboratory at Washington University where he carried research on MR compatible robotic devices and large scale research projects on child brain development (multicenter) and on multiple sclerosis. He also focused on optimization of DTI-MRI and developing a novel diffusion MR mathematical model with administrative responsibilities on the IT structure. He later joined Virginia Tech at DC, where he conducted research for the multinational (US and South Korea) Neuroperformance imaging project supported by the US Army. At the same time, he was a guest researcher at the Molecular Imaging Program at National Cancer Institute working on multimodal prostate imaging. On January 2016, Dr. Özcan joined Acıbadem Mehmet Ali Aydınlar University in Istanbul and then on October 2020 he returned to his alma mater Electrical and Electronics Engineering Dept., Boğaziçi University. Dr. Ozcan’s research interests includes mathematical modeling of diffusion MR, intravoxel incoherent motion imaging (IVIM), quantitative susceptibility mapping (QSM), radiogenomics, systems approach to functional MRI (fMRI) and magnetic hyperthermia and MR compatible robotics/devices. He is specifically interested on developing mathematical and computational methods for different pathologies in liver, glioma, breast cancer, neurodegenerative brain iron accumulation, Behçet disease, multiple sclerosis (MS) and amyotrophic lateral sclerosis (ALS). Dr. Ozcan is also working on systems science with interest in control theory and bifurcations in electrical power systems..

Burçin Ünlü obtained his BS degree from ODTÜ, MS degree from Boğaziçi University, and Ph.D. from Stevens Institute of Technology, all in Physics. After a research position at UC Irvine School of Medicine for five years, he joined the faculty of Boğaziçi University Department of Physics in 2009. He is also a Visiting Professor at GI-CoRE, Hokkaido University, Japan, since 2018. In 2017-2018, he spent one year at Stanford Medicine as a Fulbright Scholar. His research area is medical and biomedical physics, emphasizing imaging and modeling.

Cengizhan Öztürk (MD, Marmara School of Medicine, Istanbul, 1990; Ph.D., School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, 1997; postdoctoral research at Johns Hopkins BME for 3 years) is working at the Institute of Biomedical Engineering (BME), Bogazici University, Istanbul, since 2000. Dr. Ozturk managed to hold a parallel visiting research scientist position at Cardiac Interventions Program, NHLBI, NIH, for six years (2002-2008). His research at NHLBI focused on real-time MRI, XMR fusion and MR-guided medical interventions. He established Bogazici University Medical Imaging Laboratory (BUMIL), which operates now as a consortium of several labs at the Institute. Recently, Dr. Ozturk’s research focus is shifted to affordable medical imaging hardware development and coordinates Imaging Instrumentation Laboratory, Xlab (https://xlab.boun.edu.tr/). Between 2008-2013, Dr. Ozturk coordinated a university-wide effort to establish the Center for Life Sciences and Technologies (BU-LifeSci). This Center is currently in its second expansion phase of its core infrastructures: 1) microsystem-based in vivo Device Development Laboratory with its uniquely designed Clean Room, 2) Small Animal Research Center (Vivarium), 3) Smart Drugs Development Laboratory. Since 2011, Dr. Ozturk is coordinating the Istanbul Cooperation Platform for Life Sciences and Technologies (Inovita), funded initially by Istanbul Development Agency (ISTKA) which transformed itself into a thematic regional cluster, ISEK (Istanbul Health Industry Cluster). ISEK (as of January 2020) has over 180 companies (half of them startup and micro SMEs), 17 university research center, over 15 NGOs and governmental agencies. ISEK received a special 5-year cluster support grant in May 2017 from Turkish Ministry of Industry and Technology.

Esin Öztürk Işık graduated from Middle East Technical University in 1999 with a Bachelor’s degree in Computer Engineering. She received her Master’s degree from the Biomedical Engineering program of University of Alabama at Birmingham in 2002. Thereafter, Dr. Öztürk Işık was admitted to the joint Bioengineering program between the University of California at Berkeley and University of California at San Francisco. Dr. Öztürk Işık completed her Ph.D. studies in 2007 and continued her research as a postdoctoral fellow in the Radiology and Biomedical Imaging department of University of California at San Francisco. Dr. Öztürk Işık has been working as a faculty member at the Institute of Biomedical Engineering of Boğaziçi University since Fall 2014