Deniz Karakay

PhD Student

Deniz Karakay

Email: dkarakay@arizona.edu

Research: Deep learning for medical imaging, MRI reconstruction, quantitative T1/T2 mapping, and WMH segmentation/analysis.

Research Interests

My research focuses on medical image analysis and deep learning, with an emphasis on quantitative MRI and CT. I develop methods for image reconstruction, segmentation, and contrast-phase classification across multiple imaging modalities. My current interests include T1/T2 mapping, noise-robust MRI reconstruction, abdominal CT phase recognition, radiomics, and deep learning approaches for automated liver analysis. I also work on brain imaging, particularly White Matter Hyperintensity (WMH) segmentation and analyzing the relationship between vascular health and lesion burden.

Background

I am originally from Istanbul, Turkey, and completed my B.Sc. in Electrical and Electronics Engineering at Middle East Technical University (METU). In 2023, I moved to Tucson, AZ to begin my Ph.D. in Electrical and Computer Engineering at the University of Arizona.

Publications

Journal Publications

  1. S. Zahra, S. R. French, J. C. Arias, M. Ally, H. Wiskoski, C. Escareno, E. Heitkamp, F. Vazquez, M. Hillis, G. Culwell, K. Ainapurapu, C. M. Howell, K. Johnson, D. Karakay, K. Rayasam, L. Taylor, C. Kraemer, L. Leon, S. Berman, F. Yanquez, J. Balderman, J. Sabat, O. Hung, L. Lucas, E. J. Bedrick, F. Vitali, R. Mushtaq, M. Altbach, T. P. Trouard, A. Bilgin, E. M. Reiman, G. E. Alexander, & C. C. Weinkauf. In an older-age vascular cohort, carotid stenosis is associated with processing speed and executive function cognitive deficits, which correlate with p-tau217. Alzheimer’s & Dementia, 21(11): e70893, 2025. https://doi.org/10.1002/alz.70893

Conference Publications

  1. D. Karakay, H. Wiskoski, J. Peckham, J. Arias, D. Patterson, R.K. Akhbari, et al. Atherosclerosis severity in the internal carotid artery is associated with elevated white matter lesion burden in the supplied brain territories. ISMRM 2025, Honolulu, HI.

  2. D. Karakay, M. Altbach, D.R. Martin, A. Bilgin. Impact of Vessel Removal on Classification of Chronic Liver Disease using Radiomics Features and Quantitative T2 Mapping. ISMRM 2024, Singapore.

  3. Y. Zhang, A. Bilgin, S. Gokce-Kafali, B. Toner, T. Delgado, E. Ahanonu, D. Karakay, W. Zhou, et al. Enhancing Deep Learning–Based Liver Vessel Segmentation on MRI with Image Translation Techniques. ISMRM 2024, Singapore. Oral.

  4. J. Wei, D. Karakay, A. Yilmaz. A GIS-Aided Approach for Geolocalizing an Unmanned Aerial System Using Deep Learning. IEEE Sensors 2022.

Personal

Outside of research, I love exploring new places and dancing bachata and salsa. I’m also an huge movie fan and run an Instagram blog where I share film recommendations and favorite picks.

Extracurricular

I originally began my GitHub Campus Expert journey in Turkey and now continue in this role at the University of Arizona, where I support the local tech community through hackathons, open-source workshops, and student-focused talks. For the past two years, I have also served as president within the Turkish Student Association, organizing cultural events and community activities for students.