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Assistant Professor

CRCV | Center for Research in Computer Vision
University of Central Florida
4328 Scorpius St.
HEC 221
Orlando, FL 32816-2365

Phone:
Webpage: http://www.cs.ucf.edu/~bagci/
Email: bagci@ucf.edu

 
 
Prof. Bagci is a faculty member at the Center for Research in Computer Vision (CRCV), and the Assistant Professor in University of Central Florida (UCF). His research interests are Artificial intelligence, machine learning and their applications in biomedical and clinical imaging. Previously, he was a staff scientist and the lab co-manager at the NIH's Center for Infectious Disease Imaging (CIDI) Lab, department of Radiology and Imaging Sciences (RAD&IS). At NIH, Prof. Bagci has developed and implemented educational and scientific research initiatives, and mentored postdoctoral and postbaccalaureate fellows for quantitative image analysis in clinical and pre-clinical projects at the Clinical Center. Prof. Bagci had also been the leading scientist (image analyst) in biosafety/bioterrorism project initiated jointly by NIAID and IRF.

Prof. Bagci obtained his PhD degree from School of Computer Science, University of Nottingham (UK) in collaboration with Radiology department of University of Pennsylvania (with Prof. Udupa, MIPG). He has masters from Electrical Engineering and Computer Sciences and certificates of mastery from statistics, public health, and clinical trials. Prof. Bagci is senior member of IEEE and RSNA, and member of scientific organizations such as Society of Nuclear Medicine and Molecular Imaging (SNMMI), American Statistical Association (ASA), Royal Statistical Society (RSS), AAAS, and MICCAI. He has served as a program committee member for various conferences, and a regular reviewer for many prestigious journals in his fields and received best reviewer awards (most recently MICCAI 2016 Best Scientific Reviewer Award). Prof. Bagci is the recipient of many awards including NIH's FARE award (twice), RSNA Merit Certificates (5+ times), best paper awards, poster prizes, and several highlights in journal covers, media, and news. Prof. Bagci was co-chair of Image Processing Track of SPIE Medical Imaging Conference, 2017, and technical committee member of MICCAI 2018.
Capsule Networks and Explainable AI, Human-Centered AI, Optimization in Deep Learning, AI for High-Risk Applications
You can access the CRCV Publications Page for enhanced search capabilities.

2019

Khosravan, Naji; H, Celik; B, Turkbey; EC, Jones; B, Wood; Bagci, Ulas

A collaborative computer aided diagnosis (C-CAD) system with eye-tracking, sparse attentional model, and deep learning Journal Article

Medical image analysis. 2019 Jan 1;51:101-15., 2019.

BibTeX | Links:

I, Irmakci; Hussein, Sarfaraz; A, Savran; RR, Kalyani; D, Reiter; CW, Chia; KW, Fishbein; RG, Spencer; L, Ferrucci; Bagci, Ulas

A Novel Extension to Fuzzy Connectivity for Body Composition Analysis: Applications in Thigh, Brain, and Whole Body Tissue Segmentation Journal Article

IEEE Transactions on Biomedical Engineering. 2019 Apr;66(4):1069-81., 2019.

BibTeX | Links:

Bagci, Ulas; Hussein, Sarfaraz

System and method for image-based quantification of white and brown adipose tissue at the whole-body, organ and body-region levels Journal Article

United States patent application US 10/157,462. 2018 Dec 18, 2019.

BibTeX | Links:

Hussein, Sarfaraz; P, Kandel; CW, Bolan; MB, Wallace; Bagci, Ulas

Lung and pancreatic tumor characterization in the deep learning era: novel supervised and unsupervised learning approaches Journal Article

IEEE transactions on medical imaging. 2019 Jan 23., 2019.

BibTeX | Links:

H, Bogunovic; F, Venhuizen; S, Klimscha; S, Apostolopoulos; A, Bab-Hadiashar; Bagci, Ulas; MF, Beg; L, Bekalo; Q, Chen; C, Ciller; K, Gopinath

RETOUCH-The Retinal OCT Fluid Detection and Segmentation Benchmark and Challenge Journal Article

IEEE transactions on medical imaging. 2019 Feb 26., 2019.

BibTeX | Links:

DG, Vinsard; Y, Mori; M, Misawa; SE, Kudo; A, Rastogi; Bagci, Ulas; DK, Rex; MB, Wallace

Quality Assurance of Computer-Aided Detection and Diagnosis in Colonoscopy Journal Article

Gastrointestinal Endoscopy. 2019 Mar 26., 2019.

BibTeX | Links:

2017

Greena, Aileen L; Bagci, Ulas; Hussein, Sarfaraz; Kellyc, Patrick V; Muzaffara, Razi; Neuschwander-Tetrib, Brent A; Osmana, Medhat M

Brown adipose tissue detected by PET/CT imaging is associated with less central obesity Journal Article

Volume 38, , pp. pp. 629-635,, 2017.

BibTeX | Links:

Hussein, Sarfaraz; Gillies, Robert; Cao, Kunlin; Song, Qi; Bagci, Ulas

TumorNET: Lung Nodule Characterization using Multi-View Convolutional Neural Network with Gaussian Process Conference

IEEE ISBI , 2017.

BibTeX | Links:

Torosdagli, Nelisah; Liberton, Denise; Verma, Payal; Sincan, Murat; Lee, Janice; Pattanaik, Sumantha; Bagci, Ulas

Robust and Fully Automated Segmentation of Mandible from CT Scans Journal Article

IEEE ISBI 2017, 2017.

BibTeX | Links:

Greena, Aileen L; Bagci, Ulas; Hussein, Sarfaraz; Kellyc, Patrick V; Muzaffara, Razi; Neuschwander-Tetrib, Brent A; Osmana, Medhat M

Brown adipose tissue detected by PET/CT imaging is associated with less central obesity Journal Article

NuclearMedicine Communications, Volume 38, Issue 7, pp. 629-635, July, 2017.

BibTeX | Links:

Hussein, Sarfaraz; Cao, Kunlin; Song, Qi; Bagci, Ulas

Risk Stratification of Lung Nodules Using 3D CNN-Based Multi-task Learning Conference

Cornell University Library, 2017.

BibTeX | Links:

Prakash, Harish Ravi; Korostenskaja, Milena; Castillo, Eduardo; Lee, Ki; Baumgartner, James; Bagci, Ulas

Automatic Response Assessment in Regions of Language Cortex in Epilepsy Patients Using ECoG-based Functional Mapping and Machine Learning Conference

IEEE SMC, 2017.

BibTeX | Links:

Mortazi, Aliasghar; Karim, Rashed; Rhode, Kawal; Burt, Jeremy; Bagci, Ulas

CardiacNET: Segmentation of Left Atrium and Proximal Pulmonary Veins from MRI Using Multi-View CNN Conference

MICCAI 2017,, 2017.

BibTeX | Links:

Celik, H; Turkbey, B; Choyke, P; Cheng, R; McCreedy, E; McAuliffe, M; Khosravan, Naji; Bagci, Ulas; Wood, B

Eye Tracking System for Prostate Cancer Diagnosis Using Multi-Parametric MRI Conference

25th Annual Conference on ISMRM, 2017.

BibTeX | Links:

Greena, Aileen L; Bagci, Ulas; Hussein, Sarfaraz; Kellyc, Patrick V; Muzaffara, Razi; Neuschwander-Tetrib, Brent A; Osmana, Medhat M

Brown adipose tissue detected by PET/CT imaging is associated with less central obesity Journal Article

NuclearMedicine Communications, 2017.

BibTeX | Links:

2016

Hussein, Sarfaraz; Green, Aileen; Watane, Arjun; Reiter, David; Chen, Xinjian; Papadakis, Georgios Z; Wood, Bradford; Cypess, Aaron; Osman, Medhat; Bagci, Ulas

Automatic Segmentation and Quantification of White and Brown Adipose Tissues from PET/CT Scans Journal Article

IEEE Transactions on Medical Imaging, 2016.

BibTeX | Links:

Zhou, Y; Teomete, U; Dandin, O; Osman, O; Dandinoglu, T; Bagci, Ulas; Zhao, W

Computer-Aided Detection (CADx) for Plastic Deformation Fractures in Pediatric Forearm Journal Article

2016.

BibTeX | Links:

Papadakis, GZ; Millo, C; Sadowski, SM; Bagci, Ulas; Patronas, NJ

Kidney Tumor in a von Hippel-Lindau (VHL) Patient With Intensely Increased Activity on 68Ga-DOTA-TATE PET/CT Journal Article

Clinical Nuclear Medicine, 2016.

BibTeX | Links:

Papadakis, GZ; Millo, C; Sadowski, SM; Bagci, Ulas; Patronas, NJ

Epididymal Cystadenomas in von Hippel-Lindau Disease Showing Increased Activity on 68Ga DOTATATE PET/CT, Journal Article

2016.

BibTeX | Links:

Papadakis, GZ; Millo, C; Sadowski, SM; Bagci, Ulas; Patronas, NJ

Endolymphatic Sac Tumor Showing Increased Activity on 68Ga DOTATATE PET/CT Journal Article

Clinical Nuclear Medicine, 2016.

BibTeX | Links:

Johnson, Reed F; Bagci, Ulas; Keith, Lauren; Tang, Xianchun; Mollura, Daniel J; Zeitlin, Larry; Qin, Jing; Huzella, Louis; Bartos, Christopher J; Bohorova, Natasha; Bohorov, Ognian; Goodman, Charles; Kim, Do H; Paulty, Michael H; Velasco, Jesus; Whaley, Kevin J; Johnson, Joshua C; Pettitt, James; Ork, Britini L; Solomon, Jeffrey; Oberlander, Nicholas; Zhu, Quan; Sun, Jiusong; Holbrook, Michael R; Olinger, Gene G; Baric, Ralph S; Hensley, Lisa E; Jahrling, Peter B; Marasco, Wayne A

3B11-N, a monoclonal antibody against MERS-CoV, reduces lung pathology in rhesus monkeys following intratracheal inoculation of MERS-CoV Jordan-n3/2012 Journal Article

Virology, 2016.

BibTeX | Links:

Candemir, Sema; Jaeger, Stefan; Antani, Sameer; Bagci, Ulas; Folio, Les R; Xu, Ziyue; Thoma, George

Atlas-based Rib-Bone Detection in Chest X-rays Journal Article

Computerized Medical Imaging and Graphics, 2016.

BibTeX | Links:

Johnson, Reed F; Bagci, Ulas; Keith, Lauren; Tang, Xianchun; Mollura, Daniel J; Zeitlin, Larry; Qin, Jing; Huzella, Louis; Bartos, Christopher J; Bohorova, Natasha; Bohorov, Ognian; Goodman, Charles; Kim, Do H; Paulty, Michael H; Velasco, Jesus; Whaley, Kevin J; Johnson, Joshua C; Pettitt, James; Ork, Britini L; Solomon, Jeffrey; Oberlander, Nicholas; Zhu, Quan; Sun, Jiusong; Holbrook, Michael R; Olinger, Gene G; Baric, Ralph S; Hensley, Lisa E; Jahrling, Peter B; Marasco, Wayne A

3B11-N, a monoclonal antibody against MERS-CoV, reduces lung pathology in rhesus monkeys following intratracheal inoculation of MERS-CoV Jordan-n3/2012 Journal Article

2016.

BibTeX | Links:

Buty, ; M., ; Xu, Z; Gao, M; Bagci, Ulas; Wu, A; and Mollura, D

Characterization of Lung Nodule Malignancy using Hybrid Shape and Appearance Features Conference

MICCAI 2016, 2016.

BibTeX | Links:

Khosravan, Naji; Celik, Haydar; Turkbey, Baris; Cheng, Ruida; McCreedy, Evan; McAuliffe, Matthew; Sandra Bednarova, ; Jones, Elizabeth; Chen, Xinjian; Choyke, Peter L; Wood, Bradford J; Bagci, Ulas

Gaze2Segment: A Pilot Study for Integrating Eye-Tracking Technology into Medical Image Segmentation Conference

Medical Computer Vision, 2016.

BibTeX | Links:

Zhou, Y; Teomete, U; Dandin, O; Osman, O; Dandinoglu, T; Bagci, Ulas; Zhao, W

Computer-Aided Detection (CADx) for Plastic Deformation Fractures in Pediatric Forearm Journal Article

Computers in Biology and Medicine, 2016.

BibTeX | Links:

2015

Papadakis, Georgios Z; Millo, Corina; Bagci, Ulas; Sadowski, Samira M; Stratakis, Constantine A

Schmorl Nodes Can Cause Increased 68Ga DOTATATE Activity on PET/CT, Mimicking Metastasis in Patients With Neuroendocrine Malignancy Journal Article

Clinical Nuclear Medicine, 2015.

BibTeX | Links:

Becker, ; Freeman, M C; L.Vogel, ; Johnsson, J C; G.Olinger, ; J.P.Todd, ; Bagci, Ulas; Solomon, J; Mollura, D J; L.Hansley, ; Jahriling, P; Denison, M R; S.S.Rao, ; K.Subbarao, ; P.D.Kwong, ; J.R.Mascola, ; W.Kong, ; Graham, B S

Evaluation of Candidate Vaccine Approaches for MERS-CoV Journal Article

Nature Communications, 2015.

BibTeX | Links:

Camp, J V; Bagci, Ulas; Chu, Y; Squier, B; Fraig, M; Uriarte, S M; Guo, H; Mollura, D J; Jonsson, C B

Lower Respiratory Tract Infection of the Ferret by 2009 H1N1 Pandemic Influenza A Virus Triggers Biphasic Systemic and Local Neutrophil Recruitment Journal Article

Journal of Virology, 2015.

BibTeX | Links:

Xu, Ziyue; Bagci, Ulas; Foster, Brent; Mansoor, Awais; Udupa, Jayaram K; Mollura, Daniel J

A Hybrid Method for Airway Segmentation and Automated Measurement of Bronchial Wall Thickness on CT Journal Article

Medical Image Analysis, 2015.

BibTeX | Links:

Hussein, Sarfaraz; Bagci, Ulas

Transferability of 3D CNN features for Organ Detection Conference

NIPS 2015 Workshop on Machine Learning in Healthcare, 2015.

BibTeX

Gao, M; Bagci, Ulas; Lu, L; Wu, A; Buty, M; Shin, H-C; Roth, H; Papadakis, G Z; Depeursinge, A; Summers, R M; Xu, Z; Mollura, D J

Holistic Classification of CT Attenuation Patterns for Interstitial Lung Diseases via Deep Convolutional Neural Networks Conference

2015.

BibTeX | Links:

Bagci, Ulas; Papadakis, GZ; Z.Xu, ; Green, A; Osman, M; Shah, Mubarak

Nuclear Medicine Meets Computer Vision: Increasing Role of Computerized Detection, Tracking, Diagnosis, and Quantification of PET/CT and PET/MRI Studies Conference

SNMMI (Society of Nuclear Medicine and Molecular Imaging) Conference 2015, 2015.

BibTeX

Green, A; Bagci, Ulas; Kelly, PV.; Osman, M

Brown adipose tissue detected by FDG PET/CT is associated with less central obesity compared to body mass index matched controls Conference

SNMMI (Society of Nuclear Medicine and Molecular Imaging) Conference 2015., 2015.

BibTeX

Green, A; Bagci, Ulas; Kelly, PV.; Osman, M

Brown Adipose Tissue Detected by FDG PET/CT is Associated with Less Visceral Fat Conference

SNMMI (Society of Nuclear Medicine and Molecular Imaging) Conference 2015, 2015.

BibTeX

Z.Xu, ; Bagci, Ulas; Gao, M; Mollura, D J

Highly Precise Partial Volume Correction for PET Images: An Iterative Approach via Shape Consistency Conference

IEEE International Symposium of Biomedical Imaging (ISBI), 2015.

BibTeX | Links:

Papadakis, Georgios Z; Millo, Corina; Bagci, Ulas; Patronas, Nicholas J; Stratakis, Constantine A

Talc Pleurodesis with intense 18F-FDG activity but no 68Ga-DOTA-TATE activity on PET/CT Journal Article

Clinical Nuclear Medicine, 2015.

BibTeX | Links:

A.Mansoor, ; Bagci, Ulas; B.Foster, ; Z.Xu, ; Papadakis, G Z; Folio, L; Udupa, J K; Mollura, D J

Segmentation and Image Analysis of Abnormal Lungs at CT: Current Approaches, Challenges, and Future Trends Journal Article

Radiographics , 2015.

BibTeX | Links:

Papadakis, G Z; Bagci, Ulas; Sadowski, S M; Patronas, N J; Stratakis, C A

Ectopic ACTH and CRH co-secreting tumor localized by 68Ga-DOTA-TATE PET/CT Journal Article

Clinical Nuclear Medicine, 2015.

BibTeX | Links:

2014

Xu, Ziyue; Bagci, Ulas; Mansoor, Awais; Kramer-Marek, Gabriela; Luna, Brian; Kubler, Andre; Dey, Bappaditya; Foster, Brent; Papadakis, Georgios Z; Camp, Jeremy V; Jonsson, Colleen B; Bishai, William R; Jain, Sanjay; Udupa, Jayaram K; Mollura, Daniel J

Computer-aided pulmonary image analysis in small animal models Journal Article

Medical Physics, 2014.

BibTeX | Links:

2018/October: I gave a talk as a "Featured Speaker" in MICR-2018
RCAI: Radiologist-Centered AI for Lung Cancer Diagnosis
2018/October: "I joined Plos One as an Academic Editor in"
Artificial Intelligence, Deep Learning, Radiology and Imaging Sciences fields
2018/September: "Media Release (FoxTV Interview)"
Highly Accurate Lung Cancer Detection from CT Scans
2018/August: "Recent Media Releases"
Highly Accurate Lung Cancer Detection from CT Scans
2018/June: "Patent Issued"
Quantification-Brown/White, Regional, Organ, and Whole Body
2017/December: "RSNA 2017 MERIT AWARD!"
Deep Learning for Radiology Applications
2017/August: "Brain Computer Interface (BCI) 2017 Award Nomination!"
Harish's work on Deep Learning based functional mapping modality for presurgical evaluation of Epilepsy was nominated!