Dr. Ipek Oguz Profile

Dr. Ipek Oguz

Assistant Professor at Vanderbilt Univ

SPIE Involvement:

Conference Program Committee | Author

Publications (35)

Proceedings Article | 2 April 2024 Presentation + Paper

CATS v2: hybrid encoders for robust medical segmentation

Hao Li, Han Liu, Dewei Hu, Xing Yao, Jiacheng Wang, Ipek Oguz

Proceedings Volume 12926, 129260H (2024) https://doi.org/10.1117/12.3006820

KEYWORDS: Computed tomography, Image segmentation, Transformers, Windows, Medical imaging, 3D image processing, 3D modeling, Prostate, Magnetic resonance imaging, Data modeling

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Proceedings Article | 2 April 2024 Presentation + Paper

FNPC-SAM: uncertainty-guided false negative/positive control for SAM on noisy medical images

Xing Yao, Han Liu, Dewei Hu, Daiwei Lu, Ange Lou, Hao Li, Ruining Deng, Gabriel Arenas, Baris Oguz, Nadav Schwartz, Brett Byram, Ipek Oguz

Proceedings Volume 12926, 1292602 (2024) https://doi.org/10.1117/12.3006867

KEYWORDS: Image segmentation, Medical imaging, Kidney, Ultrasonography, Monte Carlo methods, Performance modeling, Image enhancement, Data modeling, Reliability, Uncertainty analysis

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Proceedings Article | 29 March 2024 Presentation + Paper

AVA: automated viewability analysis for ureteroscopic intrarenal surgery

Daiwei Lu, Yifan Wu, Xing Yao, Nicholas Kavoussi, Ipek Oguz

Proceedings Volume 12928, 129280K (2024) https://doi.org/10.1117/12.3006591

KEYWORDS: Surgery, Computed tomography, Cameras, 3D modeling, Renal calculi, Kidney, Imaging systems, Image segmentation, Endoscopes, Visualization

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Proceedings Article | 3 April 2023 Presentation + Paper

SSL2 Self-Supervised Learning meets semi-supervised learning: multiple clerosis segmentation in 7T-MRI from large-scale 3T-MRI

Jiacheng Wang, Hao Li, Han Liu, Dewei Hu, Daiwei Lu, Keejin Yoon, Kelsey Barter, Francesca Bagnato, Ipek Oguz

Proceedings Volume 12464, 124640Q (2023) https://doi.org/10.1117/12.2654522

KEYWORDS: Education and training, Magnetic resonance imaging, Multiple sclerosis, Data modeling, Image segmentation, Head, Performance modeling, Transformers, Solid state lighting, Histograms

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Proceedings Article | 3 April 2023 Presentation + Paper

Novel application of the attention mechanism on medical image harmonization

Xing Yao, Ange Lou, Hao Li, Dewei Hu, Daiwei Lu, Han Liu, Jiacheng Wang, Zachary Stoebner, Hans Johnson, Jeff Long, Jane Paulsen, Ipek Oguz

Proceedings Volume 12464, 124640Y (2023) https://doi.org/10.1117/12.2654392

KEYWORDS: Image segmentation, Medical imaging, Education and training, Content addressable memory, Control systems, Magnetic resonance imaging, Machine learning, Data modeling, White matter, Biomedical applications

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Proceedings Article | 3 April 2023 Presentation + Paper

Domain generalization for robust MS lesion segmentation

Huahong Zhang, Hao Li, Kathleen Larson, Kilian Hett, Ipek Oguz

Proceedings Volume 12464, 124640Z (2023) https://doi.org/10.1117/12.2654373

KEYWORDS: Multiple sclerosis, Image segmentation, 3D image processing, Deep learning

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Proceedings Article | 3 April 2023 Poster + Paper

Deep angiogram: trivializing retinal vessel segmentation

Dewei Hu, Xing Yao, Jiacheng Wang, Yuankai K. Tao, Ipek Oguz

Proceedings Volume 12464, 124642U (2023) https://doi.org/10.1117/12.2654214

KEYWORDS: Image segmentation, Angiography, Education and training, Principal component analysis, Photography, Data modeling, Performance modeling, Visualization, Feature extraction, Deep learning

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Proceedings Article | 4 April 2022 Presentation + Paper

Human brain extraction with deep learning

Hao Li, Qibang Zhu, Dewei Hu, Manasvi Gunnala, Hans Johnson, Omar Sherbini, Francesco Gavazzi, Russell D’Aiello, Adeline Vanderver, Jeffrey Long, Jane Paulsen, Ipek Oguz

Proceedings Volume 12032, 120321D (2022) https://doi.org/10.1117/12.2613277

KEYWORDS: Brain, Silver, 3D modeling, Magnetic resonance imaging, Image segmentation, Control systems, Neuroimaging, Tissues, Skull, Data modeling

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Proceedings Article | 4 April 2022 Presentation + Paper

Acoustic neuroma segmentation using ensembled convolutional neural networks

Qibang Zhu, Hao Li, Nathan Cass, Nathan Lindquist, Kareem Tawfik, Ipek Oguz

Proceedings Volume 12036, 120360T (2022) https://doi.org/10.1117/12.2613402

KEYWORDS: 3D modeling, Magnetic resonance imaging, Data modeling, Image segmentation, Performance modeling, Tumors, Acoustics, Convolutional neural networks, 3D magnetic resonance imaging, 3D acquisition

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Proceedings Article | 4 April 2022 Poster + Presentation + Paper

Segmentation of kidney stones in endoscopic video feeds

Zachary Stoebner, Daiwei Lu, Seok Hee Hong, Nicholas Kavoussi, Ipek Oguz

Proceedings Volume 12032, 120323G (2022) https://doi.org/10.1117/12.2613274

KEYWORDS: Video, Image segmentation, Data modeling, Renal calculi, Endoscopy, Video processing, Video acceleration, Surgery, Performance modeling, Motion models, Machine learning

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Proceedings Article | 4 April 2022 Presentation + Paper

Unsupervised denoising of retinal OCT with diffusion probabilistic model

Dewei Hu, Yuankai Tao, Ipek Oguz

Proceedings Volume 12032, 1203206 (2022) https://doi.org/10.1117/12.2612235

KEYWORDS: Denoising, Signal to noise ratio, Optical coherence tomography, Diffusion, Speckle, Image restoration, Speckle pattern, Image processing, Data modeling, Visualization

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Proceedings Article | 7 March 2022 Presentation

Deep-learning based volumetric quantification of retinal lesions in murine model of focal laser injury

Jose Rico-Jimenez, Dewei Hu, Edward Levine, Ipek Oguz, Yuankai Tao

Proceedings Volume PC11941, PC1194108 (2022) https://doi.org/10.1117/12.2607327

KEYWORDS: Injuries, Optical coherence tomography, Image segmentation, Convolutional neural networks, Tissues, Neural networks, Network architectures, In vivo imaging

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Proceedings Article | 7 March 2022 Presentation

Video-rate OCT image-enhancement using self-fusion neural network

Jose Rico-Jimenez, Dewei Hu, Eric Tang, Ipek Oguz, Yuankai Tao

Proceedings Volume PC11948, PC119481D (2022) https://doi.org/10.1117/12.2606626

KEYWORDS: Optical coherence tomography, Neural networks, Pathology, Optic nerve, Opacity, Network architectures, Image processing, Image filtering, Image acquisition, Head

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Proceedings Article | 5 March 2021 Presentation

Intraoperative spectrally encoded coherence tomography and reflectometry (iSECTR) for ophthalmic surgical guidance

Morgan Ringel, Eric Tang, Dewei Hu, Ipek Oguz, Yuankai Tao

Proceedings Volume 11630, 116300J (2021) https://doi.org/10.1117/12.2583849

KEYWORDS: Reflectometry, Tomography, Surgery, Retinal scanning, Optical coherence tomography, Microscopes, Imaging systems, Visualization, Tissues, Retinal surgery

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Proceedings Article | 15 February 2021 Presentation + Paper

Establishing surface correspondence for post-surgical cortical thickness changes in temporal lobe epilepsy

Yue Liu, Dario Englot, Victoria Morgan, Warren Taylor, Ying Wei, Ipek Oguz, Bennett Landman, Ilwoo Lyu

Proceedings Volume 11596, 115960Y (2021) https://doi.org/10.1117/12.2580808

KEYWORDS: Epilepsy, Shape analysis, Spherical lenses, Control systems, Brain, Tissues, Particles

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Proceedings Article | 15 February 2021 Presentation + Paper

MRI subcortical segmentation in neurodegeneration with cascaded 3D CNNs

Hao Li, Huahong Zhang, Hans Johnson, Jeffrey Long, Jane Paulsen, Ipek Oguz

Proceedings Volume 11596, 115960W (2021) https://doi.org/10.1117/12.2582005

KEYWORDS: Image segmentation, Magnetic resonance imaging, Neurodegeneration, Control systems, Thalamus, Neuroimaging, Medical imaging, Magnetism, Databases, Convolutional neural networks

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Proceedings Article | 15 February 2021 Poster + Presentation + Paper

Synthetic atrophy for longitudinal surface-based cortical thickness measurement

Kathleen Larson, Ipek Oguz

Proceedings Volume 11596, 115963K (2021) https://doi.org/10.1117/12.2580907

KEYWORDS: Image resolution, Tissues, Neuroimaging, Natural surfaces, Image segmentation, Brain

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Proceedings Article | 15 February 2021 Presentation + Paper

Longitudinal subcortical segmentation with deep learning

Hao Li, Huahong Zhang, Hans Johnson, Jeffrey Long, Jane Paulsen, Ipek Oguz

Proceedings Volume 11596, 115960D (2021) https://doi.org/10.1117/12.2582340

KEYWORDS: Image segmentation, Magnetic resonance imaging, Statistical analysis, 3D modeling, 3D magnetic resonance imaging

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Proceedings Article | 17 March 2020 Presentation

Joint intensity fusion with normalized cross-correlation metric for cross-modality MRI synthesis (Conference Presentation)

Kathryn Ufford, Simon Vandekar, Ipek Oguz

Proceedings Volume 11313, 1131304 (2020) https://doi.org/10.1117/12.2550009

KEYWORDS: Magnetic resonance imaging, Image fusion, Image segmentation, Detection and tracking algorithms, Medical imaging, Image processing algorithms and systems

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Proceedings Article | 10 March 2020 Presentation + Paper

Self-fusion for OCT noise reduction

Ipek Oguz, Joseph Malone, Yigit Atay, Yuankai Tao

Proceedings Volume 11313, 113130C (2020) https://doi.org/10.1117/12.2549472

KEYWORDS: Optical coherence tomography, Image fusion, Speckle, Signal to noise ratio, Denoising, Image segmentation, Image registration, Visualization, Retina, Optic nerve

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Proceedings Article | 9 March 2020 Presentation

Handheld spectrally encoded coherence tomography and reflectometry for point-of-care ophthalmic OCT and OCTA (Conference Presentation)

Eric Tang, Joseph Malone, Josh Albert Miller, Ipek Oguz, Yuankai Tao

Proceedings Volume 11228, 112280I (2020) https://doi.org/10.1117/12.2549057

KEYWORDS: Tomography, Reflectometry, Optical coherence tomography, Point-of-care devices, Imaging systems, Coherence (optics), Imaging devices, Angiography, Prototyping, Image resolution

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SPIE Journal Paper | 22 February 2020

Minimally interactive placenta segmentation from three-dimensional ultrasound images

Ipek Oguz, Natalie Yushkevich, Alison Pouch, Baris Oguz, Jiancong Wang, Shobhana Parameshwaran, James Gee, Paul Yushkevich, Nadav Schwartz

JMI, Vol. 7, Issue 01, 014004, (February 2020) https://doi.org/10.1117/12.10.1117/1.JMI.7.1.014004

KEYWORDS: Image segmentation, 3D image processing, Ultrasonography, Reliability, Image registration, Image fusion, 3D acquisition, Image processing algorithms and systems, Detection and tracking algorithms, Fetus

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SPIE Journal Paper | 3 July 2019 Open Access

Handheld spectrally encoded coherence tomography and reflectometry for motion-corrected ophthalmic optical coherence tomography and optical coherence tomography angiography

Joseph Malone, Mohamed El-Haddad, Suhaas Yerramreddy, Ipek Oguz, Yuankai K. Tao

NPh, Vol. 6, Issue 04, 041102, (July 2019) https://doi.org/10.1117/12.10.1117/1.NPh.6.4.041102

KEYWORDS: Optical coherence tomography, Coherence (optics), Tomography, Reflectometry, Imaging systems, Angiography, Optical fibers, Mirrors, Retinal scanning, In vivo imaging

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Proceedings Article | 24 February 2017 Presentation + Paper

Machine learning in a graph framework for subcortical segmentation

Zhihui Guo, Satyananda Kashyap, Milan Sonka, Ipek Oguz

Proceedings Volume 10133, 101330H (2017) https://doi.org/10.1117/12.2254874

KEYWORDS: Image segmentation, Machine learning, Neuroimaging, Magnetism, Brain, Magnetic resonance imaging, 3D modeling, Shape analysis, Tissues, Image classification, Feature extraction, Rutherfordium

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Proceedings Article | 21 March 2016 Paper

Enhanced cortical thickness measurements for rodent brains via Lagrangian-based RK4 streamline computation

Joohwi Lee, Sun Hyung Kim, Ipek Oguz, Martin Styner

Proceedings Volume 9784, 97840B (2016) https://doi.org/10.1117/12.2216420

KEYWORDS: Brain, Statistical analysis, Image analysis, Visualization, Partial differential equations, Shape analysis, Error analysis, Image processing, Brain mapping, Image segmentation, Statistical modeling

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Proceedings Article | 21 March 2016 Paper

Optimal retinal cyst segmentation from OCT images

Ipek Oguz, Li Zhang, Michael Abràmoff, Milan Sonka

Proceedings Volume 9784, 97841E (2016) https://doi.org/10.1117/12.2217355

KEYWORDS: Image segmentation, Optical coherence tomography, Retina, Retinal scanning, Data modeling, Image processing algorithms and systems, Image processing, Computer engineering

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Proceedings Article | 20 March 2015 Paper

LOGISMOS-B for primates: primate cortical surface reconstruction and thickness measurement

Ipek Oguz, Martin Styner, Mar Sanchez, Yundi Shi, Milan Sonka

Proceedings Volume 9413, 941313 (2015) https://doi.org/10.1117/12.2082327

KEYWORDS: Brain, Image segmentation, Reconstruction algorithms, Algorithm development, Magnetic resonance imaging, Tissues, Natural surfaces, Neuroimaging, 3D magnetic resonance imaging, Image processing

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Proceedings Article | 13 March 2013 Paper

DTI quality control assessment via error estimation from Monte Carlo simulations

Mahshid Farzinfar, Yin Li, Audrey Verde, Ipek Oguz, Guido Gerig, Martin Styner

Proceedings Volume 8669, 86692C (2013) https://doi.org/10.1117/12.2006925

KEYWORDS: Error analysis, Diffusion weighted imaging, Diffusion tensor imaging, Diffusion, Monte Carlo methods, Signal to noise ratio, Anisotropy, Computer simulations, Tissues, Optical spheres

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Proceedings Article | 15 March 2011 Paper

Automatic cortical thickness analysis on rodent brain

Joohwi Lee, Cindy Ehlers, Fulton Crews, Marc Niethammer, Francois Budin, Beatriz Paniagua, Kathy Sulik, Josephine Johns, Martin Styner, Ipek Oguz

Proceedings Volume 7962, 796248 (2011) https://doi.org/10.1117/12.878305

KEYWORDS: Particles, Brain, Image segmentation, Statistical analysis, Bioalcohols, Statistical modeling, Distance measurement, Diffusion, Cerebral cortex, Optimization (mathematics)

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Proceedings Article | 12 March 2011 Paper

Automatic skull-stripping of rat MRI/DTI scans and atlas building

Ipek Oguz, Joohwi Lee, Francois Budin, Ashley Rumple, Matthew McMurray, Cindy Ehlers, Fulton Crews, Josephine Johns, Martin Styner

Proceedings Volume 7962, 796225 (2011) https://doi.org/10.1117/12.878405

KEYWORDS: Brain, Image segmentation, Tissues, Magnetic resonance imaging, Diffusion tensor imaging, Neuroimaging, Image processing algorithms and systems, Binary data, 3D modeling, Image processing

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Proceedings Article | 12 March 2011 Paper

Group-wise automatic mesh-based analysis of cortical thickness

Clement Vachet, Heather Cody Hazlett, Marc Niethammer, Ipek Oguz, Joshua Cates, Ross Whitaker, Joseph Piven, Martin Styner

Proceedings Volume 7962, 796227 (2011) https://doi.org/10.1117/12.878300

KEYWORDS: Particles, Image segmentation, Brain mapping, Tissues, Statistical analysis, Brain, Binary data, Natural surfaces, Medical imaging, Analytical research

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Proceedings Article | 11 March 2011 Paper

Efficient, graph-based white matter connectivity from orientation distribution functions via multi-directional graph propagation

Alexis Boucharin, Ipek Oguz, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner

Proceedings Volume 7962, 79620S (2011) https://doi.org/10.1117/12.878291

KEYWORDS: Diffusion, Brain, Neuroimaging, 3D image processing, Image processing, Spherical lenses, Psychiatry, Medical imaging, Anisotropy, Data modeling

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Proceedings Article | 9 March 2011 Paper

Using tensor-based morphometry to detect structural brain abnormalities in rats with adolescent intermittent alcohol exposure

Beatriz Paniagua, Cindy Ehlers, Fulton Crews, Francois Budin, Garrett Larson, Martin Styner, Ipek Oguz

Proceedings Volume 7965, 79650R (2011) https://doi.org/10.1117/12.878389

KEYWORDS: Brain, Diffusion tensor imaging, Bioalcohols, Anisotropy, Neuroimaging, Image analysis, Animal model studies, Distortion, Image registration, Visualization

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Proceedings Article | 24 February 2010 Paper

Xiaoxiao Liu, Ipek Oguz, Stephen Pizer, Gig Mageras

Proceedings Volume 7625, 76252D (2010) https://doi.org/10.1117/12.843974

KEYWORDS: Lung, Tumors, Motion models, Image registration, Computed tomography, Statistical modeling, Principal component analysis, Statistical analysis, Image segmentation, Error analysis

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Proceedings Article | 26 March 2007 Paper

Statistical group differences in anatomical shape analysis using Hotelling T2 metric

Martin Styner, Ipek Oguz, Shun Xu, Dimitrios Pantazis, Guido Gerig

Proceedings Volume 6512, 65123Z (2007) https://doi.org/10.1117/12.708467

KEYWORDS: Shape analysis, Spherical lenses, Brain, Visualization, Statistical analysis, Head, 3D image processing, Binary data, Optical spheres, Neuroimaging

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Shape analysis has become of increasing interest to the neuroimaging community due to its potential to precisely locate morphological changes between healthy and pathological structures. This manuscript presents a comprehensive set of tools for the computation of 3D structural statistical shape analysis. It has been applied in several studies on brain morphometry, but can potentially be employed in other 3D shape problems. Its main limitations is the necessity of spherical topology. The input of the proposed shape analysis is a set of binary segmentation of a single brain structure, such as the hippocampus or caudate. These segmentations are converted into a corresponding spherical harmonic description (SPHARM), which is then sampled into a triangulated surfaces (SPHARM-PDM). After alignment, differences between groups of surfaces are computed using the Hotelling T² two sample metric. Statistical p-values, both raw and corrected for multiple comparisons, result in significance maps. Additional visualization of the group tests are provided via mean difference magnitude and vector maps, as well as maps of the group covariance information. The correction for multiple comparisons is performed via two separate methods that each have a distinct view of the problem. The first one aims to control the family-wise error rate (FWER) or false-positives via the extrema histogram of non-parametric permutations. The second method controls the false discovery rate and results in a less conservative estimate of the false-negatives. Prior versions of this shape analysis framework have been applied already to clinical studies on hippocampus and lateral ventricle shape in adult schizophrenics. The novelty of this submission is the use of the Hotelling T2 two-sample group difference metric for the computation of a template free statistical shape analysis. Template free group testing allowed this framework to become independent of any template choice, as well as it improved the sensitivity of our method considerably. In addition to our existing correction methodology for the multiple comparison problem using non-parametric permutation tests, we have extended the testing framework to include False Discovery Rate (FDR). FDR provides a significance correction with higher sensitivity while allowing a expected minimal amount of false-positives compared to our prior testing scheme.

Showing 5 of 35 publications

Conference Committee Involvement (6)

Image Processing

16 February 2025 | San Diego, United States

Image Processing

19 February 2024 | San Diego, California, United States

Image Processing

20 February 2023 | San Diego, California, United States

Image Processing

20 February 2022 | San Diego, California, United States

Image Processing

15 February 2021 | Online Only, California, United States

Showing 5 of 6 Conference Committees

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