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Yuanjie Zheng, Ebenezer Daniel, Allan A. Hunter III, Rui Xiao, Jianbin Gao, Hongsheng Li, Maureen  Maguire, David  Brainard, James Gee
Landmark Matching Based Retinal Image Alignment by Enforcing Sparsity in Correspondence Matrix
Medical Image Analysis (to appear)

Hongsheng Li, Yuanjie Zheng, Shaoting Zhang, Jian Chen
Solving a Special Type of Jigsaw Puzzles: Banknote Reconstruction from a Large Number of Fragments
IEEE Transactions on Multimedia (to appear)

Yuanjie Zheng, Stephen Lin, Sing Bing Kang, Rui Xiao, James C. Gee, and Chandra Kambhamettu
Single-image vignetting correction from gradient distribution symmetries
IEEE Trans. on  Pattern Analysis and Machine IntelligenceI, 35(6), 2013: 1480 - 1494.

Yuanjie Zheng, James Gee, Benjamin Backus, Kathryn Richdale
Automated Measurement of Lens Thickness Using Optical Coherence Tomography
AAO 2013: American Academy of Optometry,Myopia Mechanisms and Methods of Control on Thursday, October 24th, 2013, Seattle

Yuanjie Zheng, Dwight Stambolian, Joan O'Brien, James C. Gee
Optic Disc and Cup Segmentation from Color Fundus Photograph Using Graph Cut with Priors
MICCAI 2013: 16th International Conference on Medical Image Computing and Computer Assisted Intervention, September 22nd to 26th, 2013 in Nagoya, Japan

Yuanjie Zheng, Rui Xiao, Yan Wang, James C. Gee
A Generative Model for OCT Retinal Layer Segmentation by Integrating Graph-Based Multi-Surface Searching and Image Registration
MICCAI 2013: 16th International Conference on Medical Image Computing and Computer Assisted Intervention, September 22nd to 26th, 2013 in Nagoya, Japan

Yuanjie Zheng, Brian Vanderbeek, Ebenezer Daniel, Dwight Stambolian,  Maureen Maguire, David  Brainard, James Gee
An Automated Drusen Detection System for Classifying Age-related Macular Degeneration with Color Fundus Photographs [pdf]
ISBI 2013: International Symposium on Biomedical Imaging. 4/7 thru 4/11 2013, San Francisco, CA (Oral Presentation)

Predrag Bakic, Brad Keller, Yuanjie Zheng, Yan Wang, James Gee, Despina Kontos, Andrew Maidment;
Testing realism of software breast phantoms: texture analysis of synthetic mammograms;
In SPIE Medical Imaging 2013: Physics of Medical Imaging; Robert M. Nishikawa; Bruce R. Whiting, 28 March 2013 (Oral Presentation)

Yuanjie Zheng, Yan Wang, Brad Keller, Emily Conant, James Gee, Despina Kontos;
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;
In SPIE Medical Imaging 2013: Computer- Aided Diagnosis; Carol L. Novak; Stephen Aylward, 28 March 2013 (Oral Presentation)

Yan Wang, Brad M. Keller, Yuanjie Zheng, Raymond J. Acciavatti, James C. Gee, Andrew D. A. Maidment, Despina Kontos
The phantom study on texture feature standardization in digital mammography to improve generalizability across devices;
In SPIE Medical Imaging 2013: Computer- Aided Diagnosis; Carol L. Novak; Stephen Aylward, 28 March 2013 (Poster Presentation)

Yuanjie Zheng, Brian Vanderbeek, Rui Xiao, Ebenezer Daniel, Dwight Stambolian,  Maureen Maguire, Joan O'Brien, James Gee
Retrospective Illumination Correction of Retinal Fundus images from Gradient Distribution Sparsity [pdf]
ISBI 2012: International Symposium on Biomedical Imaging. 5/2 thru 5/5 2012, Barcelona, Spain (Oral Presentation)

Yan Wang, Brad M. Keller, Yuanjie Zheng, Raymond J. Acciavatti, James C. Gee, Andrew D. A. Maidment and Despina Kontos
Phantom Study for Assessing the Effect of Different Digital Detectors on Mammographic Texture Features
Lecture Notes in Computer Science, 2012, Volume 7361/2012, 604-610

J. Wu, K. Davis, Yuanjie Zheng, H. Wang, B. Litt, and J. Gee
Brain Parcellation Aids in Electrode Localization in Epileptic Patients
MICCAI 2011 Workshop on Augmented Environments for Computer-Assisted Interventions, 9/18 thru 9/22, 2011 Toronto, Canada

Yuanjie Zheng, Diane Nathan; Yan Wang; Brad Keller; Emily Conant; James Gee; Despina Kontos
Pectoral Muscle Identification in Mammograms with a Layout Consistent Markov Random Field
MICCAI 2011 Workshop on Breast Image Analysis, 9/18 thru 9/22, 2011 Toronto, Canada (Oral Presentation)

B. Keller, D. Li, Y. Wan, Yuanjie Zheng, J. C. Gee, E.C. Conant, and D. Kontos: Adaptive Multi-Cluster Fuzzy C-Means Segmentation of Breast Parenchymal Tissue in Digital Mammography.
MICCAI 2011, 9/18 thru 9/22, 2011 Toronto, Canada

Yuanjie Zheng, B. Keller, Y. Wang, N. Tustison, G. Song, P.R. Bakic, A.D. Maidment, E.F. Conant, J.C. Gee, D. Kontos
A Fully-Automated Software Pipeline for Parenchymal Pattern Analysis in Digital Breast Images: Towards the Translation of Imaging Biomarkers in Routine Breast Cancer Risk Assessment
RSNA (Radiological Society of North America) 2011 Annual Meeting and Scientific Assembly: Showcase on the 2011 Quantitative Imaging Reading Room, 1/27 thru 12/2, 2011 Chicago, IL (Oral Presentation)

Yuanjie Zheng, Allan A. Hunter III, Jue Wu, Hongzhi Wang, Jianbin Gao, Maureen G. Maguire, James C. Gee,
Landmark Matching Based Automatic Retinal Image Registration with Linear Programming and Self-Similarities
IPMI 2011: International Conference on Information Processing in Medical Imaging, July 3-8, 2011, Monastery Irsee, Germany (Bavaria)

Yuanjie Zheng,  Hongzhi Wang, Jue Wu, Jianbin Gao, James C. Gee,
Multiscale Analysis Revisited: Detection of Drusen and Vessel in Digital Retinal Images
ISBI 2011: IEEE International Symposium on Biomedical Imaging, March 30 - April 2, 2011, Chicago, Illinois, USA

Nicholas J. Tustison, Brian B. Avants, Philip A. Cook, Yuanjie Zheng, Alexander Egan, Paul A. Yushkevich, James C. Gee
N4ITK: Improved N3 Bias Correction.
IEEE Trans. Med. Imaging 29(6): 1310-1320 (2010)

Brian B. Avants, Philip A. Cook, Corey McMillan, Murray Grossman, Nicholas J. Tustison, Yuanjie Zheng, James C. Gee
Sparse Unbiased Analysis of Anatomical Variance in Longitudinal Imaging.
MICCAI (1) 2010: 324-331

Yuanjie Zheng, James Gee,
Estimation of Image Bias Field with Sparsity Constraints, [PDF][code]
CVPR 2010: IEEE Computer Society Conf. on Computer Vision and Pattern Recognition. San Francisco, CA, June 13-18, 2010

Yuanjie Zheng, Andrew D. A. Maidment, James Gee
Accurate Registration of Dynamic Contrast-Enhanced Breast MR images with Robust Estimation and Linear Programming, [PDF]
ISBI 2010: IEEE International Symposium on Biomedical Imaging, April 14-17, 2010, Rotterdam, The Netherlands. (oral presentation)

Yuanjie Zheng, Murray Grossman, Suyash Awate, James Gee
Automatic Correction of Intensity Nonuniformity From Sparseness of Gradient Distribution in Medical Images
MICCAI 2009: the 12th International Conference on Medical Image Computing and Computer Assisted Intervention, London, UK, September 20-24, 2009  [PDF][code]

Yuanjie Zheng, Chandra Kambhamettu
Learning Based Digital Matting
ICCV 2009: The 20th IEEE International Conference on Computer Vision. Kyoto, Japan, Sep. 29-Oct. 2, 2009 [PDF][code]

Yuanjie Zheng, Chandra Kambhamettu, Stephen Lin,
Single-Image Optical Center Estimation from Vignetting and Tangential Gradient Symmetry, [PDF][code]
CVPR 2009: IEEE Computer Society Conf. on Computer Vision and Pattern Recognition. Miami, Florida, June 20-25, 2009

Yuanjie Zheng, Chandra Kambhamettu, Thomas L. Bauer, Karl Steiner,
Accurate Estimation of Pulmonary Nodule's Growth Rate in CT Images with Nonrigid Registration and Precise Nodule Detection and Segmentation [PDF]
MMBIA 2009: Mathematical Methods in Biomedical Image Analysis, Miami, Florida, June 20, 2009

Yuanjie Zheng, Sarah Englander, Sajjad Baloch, Evangelia I. Zacharaki, Yong Fan, Mitchell D. Schnall, Dinggang Shen
STEP: Spatio-Temporal Enhancement Pattern, for MR-based Breast Tumor Diagnosis,[PDF][code]
Medical Physics 36(7), 2009: 3192-3204 (chosen to appear on the cover)

Yuanjie Zheng, Stephen Lin, Chandra Kambhamettu, Jingyi Yu, Sing Bing Kang
Single-Image Vignetting Correction, [PDF][code]
IEEE Trans. on  Pattern Analysis and Machine Intelligence, 31(12), 2243-2256, 2009.

Hui Qiao, Hualei Zhang, Yuanjie Zheng, Datta E. Ponde, Dinggang Shen, Fabao Gao, Ashley Bakken, Alexander Schmitz, Hank F Kung, Victor A. Ferrari, and Rong Zhou
MRI and PET dual detection for serial assessment of embryonic stem cells grafted in normal and infarcted myocardium
Radiology (to Appear)

Yuanjie Zheng, Chandra Kambhamettu, Thomas Bauer, Karl Steiner,
Estimation of Ground-Glass Opacity Measurement in CT Lung Images, [PDF]
MICCAI 2008: International Conference on Medical Image Computing and Computer Assisted Intervention, New York City, USA, September, 2008.

Yuanjie Zheng, Jingyi Yu, Sing Bing Kang, Stephen Lin, Chandra Kambhamettu,
Single-Image Vignetting Correction Using Radial Gradient Symmetry,[PDF][code]
Oral Presentation on CVPR 2008: IEEE Computer Society Conf. on Computer Vision and Pattern Recognition.

Yuanjie Zheng, Chandra Kambhamettu, Jingyi Yu, Thomas Bauer, Karl Steiner,
FuzzyMatte: A Computationally Efficient Scheme for Interactive Matting, PDF + (Supplementary_Proofs) [code]
Poster Presentation on CVPR 2008: IEEE Computer Society Conf. on Computer Vision and Pattern Recognition.

Yuanjie Zheng, Karl Steiner, Thomas L. Bauer, Jingyi Yu, Dinggang Shen, Chandra Kambhamettu,
Lung Nodule Growth Analysis from 3D CT Data with a Coupled Segmentation and Registration Framework, (PDF)
MMBIA 2007: IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis, Rio de Janeiro, Brasil, Oct 14-15, 2007.

Yuanjie Zheng, Sajjad Baloch, Sarah Englander, Mitchell D. Schnall, Dinggang Shen,
Segmentation and Classification of Breast Tumor Using Dynamic Contrast-Enhanced MR Image, [PDF][code]
MICCAI 2007: International Conference on Medical Image Computing and Computer Assisted Intervention, Brisbane, Australia, November 2007.

Yuanjie Zheng, Jingyi Yu, Chandra Kambhamettu, Sarah Englander, Mitchell D. Schnall, Dinggang Shen
De-enhancing the Dynamic Contrast-Enhanced Breast MRI for Robust Registration, (PDF)
MICCAI 2007: International Conference on Medical Image Computing and Computer Assisted Intervention, Brisbane, Australia, November 2007.

Yuanjie Zheng, Sarah Englander, Mitchell D. Schnall, Dinggang Shen
STEP: Spatial-Temporal Enhancement Pattern, for MR-based Breast Tumor Diagnosis, [PDF][code]
ISBI 2007: IEEE International Symposium on Biomedical Imaging, April 12-15, 2007, Metro Washington, D.C., USA. (oral presentation)

Yuanjie Zheng, Stephen Lin, Sing Bing Kang
Single-Image Vignetting Correction, (PDF)
CVPR 2006: IEEE Computer Society Conf. on Computer Vision and Pattern Recognition, June 2006, vol. 1, pp. 461-468. (oral presentation).

Yuanjie Zheng, Jie Yang, Yun Zhu, Lixiu Yao
Fuzzy Region Competition, (PDF)
Unpublished and finished in 2003.

Yuanjie Zheng, Sarah Englander, Mitchell D. Schnall, Dinggang Shen
STEP: Spatial-Temporal Enhancement Pattern, and Features for MR-based Breast Tumor Diagnosis
In revisions for IEEE Transaction on Medical Imaging

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