Dr. James C. Gee Profile

Dr. James C. Gee

Professor at Univ of Pennsylvania

SPIE Involvement:

Conference Program Committee | Author

Publications (39)

Proceedings Article | 2 April 2024 Presentation + Paper

Automated estimation of microcirculation capillary density using relative perfusion maps

Rohit Jena, Yifan Wu, John Greenwood, Pratik Chaudhari, James Gee

Proceedings Volume 12926, 129260U (2024) https://doi.org/10.1117/12.3000736

KEYWORDS: Capillaries, Video, Image segmentation, Education and training, Red blood cells, Plasma, Binary data, Video microscopy, Surgery, Neural networks

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Proceedings Article | 7 April 2023 Presentation + Paper

Integrating color deconvolution thresholding and weakly supervised learning for automated segmentation of neurofibrillary tangle and neuropil threads

Hyung Roh, David Irwin, Mónica Muñoz López, Maria Mercedes Iñiguez de Onzoño Martin, Ranjit Ittyerah, Sydney Lim, Madigan Bedard, John Robinson, Theresa Schuck, Emilio Artacho-Pérula, María del Mar Arroyo Jiménez, María Pilar Marcos Rabal, Francisco Javier Molina Romero, Sandra Cebada Sánchez, José Carlos Delgado González, Carlos de la Rosa-Prieto, Marta Córcoles Parada, Edward Lee, Daniel Ohm, Laura E. Wisse, David Wolk, James Gee, Ricardo Insausti, Paul Yushkevich, Min Chen

Proceedings Volume 12471, 1247103 (2023) https://doi.org/10.1117/12.2651848

KEYWORDS: Image segmentation, Proteins, Education and training, Histopathology, Machine learning, RGB color model, Pathology, Image deconvolution, Data modeling, Cross validation

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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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Proceedings Article | 6 March 2018 Paper

Bayesian network interface for assisting radiology interpretation and education

Jeffrey Duda, Emmanuel Botzolakis, Po-Hao Chen, Suyash Mohan, Ilya Nasrallah, Andreas Rauschecker, Jeffrey Rudie, R. Nick Bryan, James Gee, Tessa Cook

Proceedings Volume 10579, 105790S (2018) https://doi.org/10.1117/12.2293691

KEYWORDS: Diagnostics, Magnetic resonance imaging, Radiology, Databases, Diffusion, Brain, Data modeling, Basal ganglia, Bayesian inference, Neuroimaging

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Proceedings Article | 29 March 2016 Paper

Automatic segmentation of canine retinal OCT using adaptive gradient enhancement and region growing

Yufan He, Yankui Sun, Min Chen, Yuanjie Zheng, Hui Liu, Cecilia Leon, William Beltran, James Gee

Proceedings Volume 9788, 97881Q (2016) https://doi.org/10.1117/12.2217186

KEYWORDS: Image segmentation, Optical coherence tomography, Retina, Therapeutics, Clinical trials, Image resolution, Digital filtering, Image filtering, Algorithm development, Analytical research

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SPIE Journal Paper | 3 April 2015

Parenchymal texture analysis in digital mammography: robust texture feature identification and equivalence across devices

Brad Keller, Andrew Oustimov, Yan Wang, Jinbo Chen, Raymond Acciavatti, Yuanjie Zheng, Shonket Ray, James Gee, Andrew D. Maidment, Despina Kontos

JMI, Vol. 2, Issue 02, 024501, (April 2015) https://doi.org/10.1117/12.10.1117/1.JMI.2.2.024501

KEYWORDS: Lawrencium, Digital mammography, Breast, Imaging systems, Breast cancer, Sensors, Computing systems, Mammography, Tissues, Image segmentation

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Proceedings Article | 29 March 2013 Paper

The ANTs cortical thickness processing pipeline

Nicholas Tustison, Brian Avants, Philip Cook, Gang Song, Sandhitsu Das, Niels van Strien, James Stone, James Gee

Proceedings Volume 8672, 86720K (2013) https://doi.org/10.1117/12.2007128

KEYWORDS: Brain, Neuroimaging, Data modeling, Image segmentation, Image registration, Brain mapping, Medical imaging, Neuroscience, Skull, Magnetic resonance imaging

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Proceedings Article | 29 March 2013 Paper

Statistical bias in optimized VBM

Nicholas Tustison, Brian Avants, Philip Cook, James Gee, James Stone

Proceedings Volume 8672, 86720U (2013) https://doi.org/10.1117/12.2006377

KEYWORDS: Statistical analysis, Error analysis, Analytical research, Image segmentation, Medical imaging, Neuroscience, Neuroimaging, Anisotropy, Brain, Image processing

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Proceedings Article | 19 March 2013 Paper

Testing realism of software breast phantoms: texture analysis of synthetic mammograms

Predrag Bakic, Brad Keller, Yuanjie Zheng, Yan Wang, James Gee, Despina Kontos, Andrew Maidment

Proceedings Volume 8668, 866824 (2013) https://doi.org/10.1117/12.2008173

KEYWORDS: Breast, Mammography, Tissues, Software development, Breast imaging, Image analysis, Imaging systems, X-rays, Computer simulations, Ions

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Proceedings Article | 28 February 2013 Paper

A fully-automated software pipeline for integrating breast density and parenchymal texture analysis for digital mammograms: parameter optimization in a case-control breast cancer risk assessment study

Yuanjie Zheng, Yan Wang, Brad Keller, Emily Conant, James Gee, Despina Kontos

Proceedings Volume 8670, 86701B (2013) https://doi.org/10.1117/12.2008155

KEYWORDS: Breast, Breast cancer, Tissues, Digital mammography, Mammography, Image classification, Cancer, Image segmentation, Software development, Machine vision

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Proceedings Article | 28 February 2013 Paper

Texture feature standardization in digital mammography for improving generalizability across devices

Yan Wang, Brad Keller, Yuanjie Zheng, Raymond Acciavatti, James Gee, Andrew D. A. Maidment, Despina Kontos

Proceedings Volume 8670, 867026 (2013) https://doi.org/10.1117/12.2008149

KEYWORDS: Breast, Imaging systems, Breast cancer, Sensors, Digital mammography, Feature extraction, Image processing, Modulation transfer functions, Control systems, Spatial resolution

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Growing evidence suggests a relationship between mammographic texture and breast cancer risk. For studies performing texture analysis on digital mammography (DM) images from various DM systems, it is important to evaluate if different systems could introduce inherent differences in the images analyzed and how to construct a methodological framework to identify and standardize such effects, if these differences exist. In this study, we compared two DM systems, the GE Senographe 2000D and DS using a validated physical breast phantom (Rachel, Gammex). The GE 2000D and DS systems use the same detector, but a different automated exposure control (AEC) system, resulting in differences in dose performance. On each system, images of the phantom are acquired five times in the Cranio-Caudal (CC) view with the same clinically optimized phototimer setting. Three classes of texture features, namely grey-level histogram, cooccurrence, and run-length texture features (a total of 26 features), are generated within the breast region from the raw DM images and compared between the two imaging systems. To alleviate system effects, a range of standardization steps are applied to the feature extraction process: z-score normalization is performed as the initial step to standardize image intensities, and the parameters in generating co-occurrence features are varied to decrease system differences introduced by detector blurring effects. To identify texture features robust to detectors (i.e. the ones minimally affected only by electronic noise), the distribution of each texture feature is compared between the two systems using the Kolmogorov-Smirnov (K-S) test at 0.05 significance, where features with p>0.05 are deemed robust to inherent system differences. Our approach could provide a basis for texture feature standardization across different DM imaging systems and provide a systematic methodology for selecting generalizable texture descriptors in breast cancer risk assessment.

Proceedings Article | 9 March 2010 Paper

Qiang Wang, Amalia Charisi, Longin Jan Latecki, James Gee, Vasilis Megalooikonomou

Proceedings Volume 7624, 762428 (2010) https://doi.org/10.1117/12.844319

KEYWORDS: Shape analysis, Control systems, Medical imaging, Detection and tracking algorithms, Stars, Image analysis, Brain, Medical diagnostics, Magnetic resonance imaging, Information science

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Proceedings Article | 15 May 2003 Paper

Tensor scale-based image registration

Punam Saha, Hui Zhang, Jayaram Udupa, James Gee

Proceedings Volume 5032, (2003) https://doi.org/10.1117/12.481433

KEYWORDS: Image registration, Anisotropy, Magnetic resonance imaging, Image segmentation, Neuroimaging, Brain, Image compression, Medical imaging, Principal component analysis, 3D modeling

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Proceedings Article | 15 May 2003 Paper

A method for non-rigid registration of diffusion tensor magnetic resonance images

Jeffrey Duda, Mariano Rivera, Daniel Alexander, James Gee

Proceedings Volume 5032, (2003) https://doi.org/10.1117/12.481155

KEYWORDS: Diffusion, Signal to noise ratio, Image registration, Surface conduction electron emitter displays, Anisotropy, Magnetism, Tissues, Associative arrays, Radiology, In vivo imaging

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Proceedings Article | 15 May 2003 Paper

Two algorithms for non-rigid image registration and their evaluation

Zhiyong Xie, Lydia Ng, James Gee

Proceedings Volume 5032, (2003) https://doi.org/10.1117/12.481381

KEYWORDS: Image registration, Brain, Image segmentation, Algorithm development, Neuroimaging, Medical imaging, Image resolution, Magnetic resonance imaging, Cerebellum, Amygdala

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SPIE Journal Paper | 1 January 2003

Bayesian model for intensity mapping in magnetic resonance imaging image registration

Alexei Machado, Mario Campos, James Gee

JEI, Vol. 12, Issue 01, (January 2003) https://doi.org/10.1117/12.10.1117/1.1526845

KEYWORDS: Image registration, Tissues, Scanners, Magnetic resonance imaging, Image segmentation, Image processing, Instrument modeling, Associative arrays, Data modeling, Neuroimaging

SPIE Journal Paper | 1 January 2003 Open Access

Guest Editorial: Model-based Medical Image Processing and Analysis

James Gee, Mostafa Analoui

JEI, Vol. 12, Issue 01, (January 2003) https://doi.org/10.1117/12.10.1117/1.1543561

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Proceedings Article | 9 May 2002 Paper

Novel spatial interaction prior for Bayesian image segmentation and restoration

Mariano Rivera, James Gee

Proceedings Volume 4684, (2002) https://doi.org/10.1117/12.467052

KEYWORDS: Image segmentation, Chromium, Tissues, Data modeling, Image processing algorithms and systems, Brain, Optimization (mathematics), Magnetic resonance imaging, Magnetorheological finishing, Head

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Proceedings Article | 9 May 2002 Paper

Method for quantitative assessment of atherosclerotic lesion burden on the basis of high-resolution black-blood MRI

Jeffrey Duda, Hee Song, Ronald Wolf, Alex Wright, James Gee, Felix Wehrli

Proceedings Volume 4684, (2002) https://doi.org/10.1117/12.467154

KEYWORDS: Arteries, Magnetic resonance imaging, Signal to noise ratio, Image processing, Scanning electron microscopy, Tissues, Image segmentation, Binary data, Algorithm development, Error analysis

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Proceedings Article | 9 May 2002 Paper

Validation of a nonrigid registration algorithm for multimodal data

Peter Rogelj, Stanislav Kovacic, James Gee

Proceedings Volume 4684, (2002) https://doi.org/10.1117/12.467170

KEYWORDS: Image registration, Image segmentation, Image quality, Tissues, Image restoration, Magnetic resonance imaging, Brain, Medical imaging, Image transmission, Gold

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Proceedings Article | 9 May 2002 Paper

Soft parametric curve matching in scale-space

Brian Avants, James Gee

Proceedings Volume 4684, (2002) https://doi.org/10.1117/12.467071

KEYWORDS: Annealing, Computer programming, Algorithm development, Detection and tracking algorithms, Data modeling, Stochastic processes, Reliability, Gaussian filters, Image segmentation, 3D image processing

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Proceedings Article | 3 July 2001 Paper

Validation of brain segmentation and tissue classification algorithm for T1-weighted MR images

Vikram Chalana, Lydia Ng, Larry Rystrom, James Gee, David Haynor

Proceedings Volume 4322, (2001) https://doi.org/10.1117/12.431079

KEYWORDS: Brain, Image segmentation, Tissues, Neuroimaging, Image processing algorithms and systems, Magnetic resonance imaging, Algorithm development, Image registration, Image classification, Head

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Proceedings Article | 3 July 2001 Paper

Factor analysis of high-dimensional heterogeneous data for structural characterization

Alexei Machado, James Gee, Mario Campos

Proceedings Volume 4322, (2001) https://doi.org/10.1117/12.431098

KEYWORDS: Factor analysis, Statistical analysis, Principal component analysis, Control systems, Pathology, Statistical modeling, Image registration, Image processing, Medical diagnostics, Magnesium

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Proceedings Article | 3 July 2001 Paper

Characterizing populations and searching for diagnostics via elastic registration of MRI images

David Pettey, James Gee

Proceedings Volume 4322, (2001) https://doi.org/10.1117/12.431049

KEYWORDS: Magnetic resonance imaging, Diagnostics, Image registration, Image restoration, Medical imaging, Image processing, Image classification

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Proceedings Article | 3 July 2001 Paper

Segmentation of cerebral MRI scans using a partial volume model, shading correction, and an anatomical prior

Aljaz Noe, Stanislav Kovacic, James Gee

Proceedings Volume 4322, (2001) https://doi.org/10.1117/12.431028

KEYWORDS: Image segmentation, Tissues, Photovoltaics, Magnetic resonance imaging, Image processing algorithms and systems, Brain, Neuroimaging, Image processing, Image registration, Neodymium

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Proceedings Article | 6 June 2000 Paper

Exploratory and confirmatory factor analysis in morphometry

Alexei Machado, James Gee, Mario Campos

Proceedings Volume 3979, (2000) https://doi.org/10.1117/12.387734

KEYWORDS: Factor analysis, Principal component analysis, Image registration, Control systems, Statistical analysis, Magnetic resonance imaging, Image processing, Magnesium, Brain, Analytical research

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Proceedings Article | 6 June 2000 Paper

Performance evaluation of medical image processing algorithms

James Gee

Proceedings Volume 3979, (2000) https://doi.org/10.1117/12.387682

KEYWORDS: Databases, Image processing, Algorithm development, Image registration, Medical imaging, Systems modeling, Image analysis, Medical research, Brain, Analytical research

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Proceedings Article | 6 June 2000 Paper

Techniques for spatial normalization of diffusion tensor images

Daniel Alexander, C. Pierpaoli, P. Basser, James Gee

Proceedings Volume 3979, (2000) https://doi.org/10.1117/12.387708

KEYWORDS: Brain, Diffusion, Tissues, Anisotropy, Neuroimaging, Statistical analysis, Optical spheres, Image registration, Image processing, 3D image processing

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Proceedings Article | 21 May 1999 Paper

Likelihood estimation in image warping

Alexei Machado, Mario Campos, James Gee

Proceedings Volume 3661, (1999) https://doi.org/10.1117/12.348615

KEYWORDS: Magnetic resonance imaging, Tissues, Scanners, Image analysis, Information technology, Data acquisition, Image sensors, Image processing, Image registration, Magnesium

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Proceedings Article | 21 May 1999 Paper

New experimental results in atlas-based brain morphometry

James Gee, Brian Fabella, Siddharth Fernandes, Bruce Turetsky, Ruben Gur, Raquel Gur

Proceedings Volume 3661, (1999) https://doi.org/10.1117/12.348616

KEYWORDS: Brain, Neuroimaging, Control systems, Shape analysis, Magnetic resonance imaging, Statistical analysis, Image segmentation, Transform theory, Digital imaging, Brain mapping

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Proceedings Article | 24 June 1998 Paper

Atlas warping for brain morphometry

Alexei Machado, James Gee

Proceedings Volume 3338, (1998) https://doi.org/10.1117/12.310942

KEYWORDS: Brain, Shape analysis, Principal component analysis, Statistical analysis, Image processing, Magnesium, Image segmentation, Image registration, Magnetic resonance imaging, Tin

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Proceedings Article | 25 April 1997 Paper

Effect of spatial normalization on analysis of functional data

James Gee, David Alsop, Geoffrey Aguirre

Proceedings Volume 3034, (1997) https://doi.org/10.1117/12.274142

KEYWORDS: Magnetic resonance imaging, Brain, Brain mapping, Functional magnetic resonance imaging, Image registration, Neuroimaging, Image resolution, Statistical analysis, Spatial resolution, Chemical elements

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Proceedings Article | 25 April 1997 Paper

Robust partial-volume tissue classification of cerebral MRI scans

Lucien Nocera, James Gee

Proceedings Volume 3034, (1997) https://doi.org/10.1117/12.274118

KEYWORDS: Tissues, Magnetic resonance imaging, Image segmentation, Brain, Neuroimaging, 3D modeling, Signal to noise ratio, Image classification, Magnetism, Visual analytics

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Proceedings Article | 16 April 1996 Paper

Rapid coarse-to-fine matching using scale-specific priors

James Gee, David Haynor

Proceedings Volume 2710, (1996) https://doi.org/10.1117/12.237944

KEYWORDS: Image segmentation, Magnetic resonance imaging, Head, Thalamus, Brain, Information technology, Chemical elements, Neuroimaging, Data modeling, Infrared imaging

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Proceedings Article | 12 May 1995 Paper

Bayesian approach to the brain image matching problem

James Gee, Lionel Le Briquer, Christian Barillot, David Haynor, Ruzena Bajcsy

Proceedings Volume 2434, (1995) https://doi.org/10.1117/12.208686

KEYWORDS: Brain mapping, Brain, Associative arrays, Neuroimaging, Error analysis, Tissues, Data modeling, Information technology, Image classification, Infrared imaging

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Proceedings Article | 9 September 1994 Paper

Matching structural images of the human brain using statistical and geometrical image features

James Gee, Christian Barillot, Lionel Le Briquer, David Haynor, Ruzena Bajcsy

Proceedings Volume 2359, (1994) https://doi.org/10.1117/12.185179

KEYWORDS: Brain, Neuroimaging, Chemical elements, Tissues, Image registration, Image classification, Image fusion, Image resolution, Information technology, Image filtering

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Proceedings Article | 11 May 1994 Paper

Finite element approach to warping of brain images

James Gee, David Haynor, Martin Reivich, Ruzena Bajcsy

Proceedings Volume 2167, (1994) https://doi.org/10.1117/12.175067

KEYWORDS: Chemical elements, Brain, Neuroimaging, Probability theory, Image processing, Information technology, 3D image processing, Finite element methods, Brain mapping, Magnetic resonance imaging

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Proceedings Article | 1 June 1992 Paper

Quantitative analysis of cerebral images using an elastically deformable atlas: theory and validation

James Gee, Martin Reivich, Ruzena Bajcsy

Proceedings Volume 1652, (1992) https://doi.org/10.1117/12.59433

KEYWORDS: Brain, Neuroimaging, Image processing, Medical imaging, Positron emission tomography, Magnetic resonance imaging, Computed tomography, 3D image processing, Quantitative analysis, Image registration

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Proceedings Article | 1 June 1991 Paper

Evaluation of multiresolution elastic matching using MRI data

James Gee, Martin Reivich, L. Bilaniuk, David Hackney, R. Zimmerman, Stanislav Kovacic, Ruzena Bajcsy

Proceedings Volume 1445, (1991) https://doi.org/10.1117/12.45220

KEYWORDS: Brain, Magnetic resonance imaging, Neuroimaging, Computing systems, Computed tomography, Positron emission tomography, X-ray computed tomography, Image processing, 3D image processing, Thalamus

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Showing 5 of 39 publications

Conference Committee Involvement (24)

Image Processing

16 February 2025 | San Diego, California, 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

Image Processing

17 February 2020 | Houston, Texas, United States

Image Processing

19 February 2019 | San Diego, California, United States

Image Processing

11 February 2018 | Houston, Texas, United States

Image Processing

12 February 2017 | Orlando, Florida, United States

Image Processing Posters

12 February 2017 | Orlando, FL, United States

Image Processing

1 March 2016 | San Diego, California, United States

Image Processing

24 February 2015 | Orlando, Florida, United States

Image Processing

16 February 2014 | San Diego, California, United States

Image Processing

10 February 2013 | Lake Buena Vista (Orlando Area), Florida, United States

Image Processing

6 February 2012 | San Diego, California, United States

Image Processing

14 February 2011 | Lake Buena Vista (Orlando), Florida, United States

Image Processing

14 February 2010 | San Diego, California, United States

Image Processing

8 February 2009 | Lake Buena Vista (Orlando Area), Florida, United States

Image Processing

17 February 2008 | San Diego, California, United States

Image Processing

18 February 2007 | San Diego, CA, United States

Image Processing

13 February 2006 | San Diego, California, United States

Image Processing

14 February 2005 | San Diego, California, United States

Image Processing

16 February 2004 | San Diego, California, United States

Image Processing

17 February 2003 | San Diego, California, United States

Showing 5 of 24 Conference Committees

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