Publications

Book Chapters

Joshua Cates, Shireen Y. Elhabian, Ross T. Whitaker. ShapeWorks: Particle-based shape correspondence and visualization software. In Statistical Shape and Deformation Analysis: Methods, Implementation and Applications. 1st Edition, Academic Press, 2017.
ShapeWorksStudio
ShapeWorks command line tools
Please visit my tutorials for a hands-on lab.

Refereed Journal Publications

Benjamin A Orkild, Brian Zenger, Krithika GS Iyer, Lindsay C Rupp, Masjid M Ibrahim, Atefeh G Khashani, Maura D Perez, Marcus D Foote, Jake A Bergquist, Alan K Morris, Ji- won J Kim, Benjamin A Steinberg, Craig Selzman, Mark B Ratcliffe, Rob S MacLeod, Shireen Elhabian (co-senior author), Ashley E Morgan. All Roads Lead to Rome: Diverse Etiologies of Tricuspid Regurgitation Create a Predictable Constellation of Right Ventricular Shape Changes. Frontiers in Physiology, 13, pp. 1092, 2022.

Anupama Goparaju, Alexandre Bone, Nan Hu, Heath B. Henninger, Andrew E. Anderson, Stanley Durrleman, Matthijs Jacxsens, Alan Morris, Ibolya Csecs, Nassir Marrouche, Shireen Y. Elhabian. Benchmarking Off-the-Shelf Statistical Shape Modeling Tools in Clinical Applications. Medical Image Analysis, 76, 2022.

Penny R. Atkins, Praful Agrawal, Joseph D. Mozingo, Keisuke Uemura, Kunihiko Tokunaga, Christopher L. Peters, Shireen Y. Elhabian, Ross T. Whitaker, Andrew E. Anderson. Prediction of Femoral Head Coverage from Articulated Statistical Shape Models of Patients with Develop- mental Dysplasia of the Hip. Journal of Orthopaedic Research, pp. 1-14, 2021.

Riddhish Bhalodia, Shireen Elhabian, Ladislav Kavan, Ross Whitaker. Leveraging Unsupervised Image Registration for Discovery of Landmark Shape Descriptor. Medical Image Analysis, 1(73), pp. 102-157, 2021.

Praful Agrawal, Ross Whitaker, Shireen Y. Elhabian. An Optimal, Generative Model for Estimating Multi-label Probabilistic Maps. IEEE Transaction of Medical Imaging, vol. 39, no. 7, pp. 2316-2326, 2020.

Wei Xing, Shireen Y. Elhabian, Vahid Keshavarzzadeh, Robert M. Kirby. Shared-GP: Learning Interpretable Shared Hidden Structure Across Data Spaces for Design Space Analysis and Exploration. ASME Journal of Mechanical Design, pp. 1-16, 2020.

Matthijs Jacxsens, Shireen Y. Elhabian, Sarah Brady, Peter Chalmers, Andreas Mueller, Robert Tashjian, Heath Henninger. Thinking outside the glenohumeral box: Hierarchical shape variation of the periarticular anatomy of the scapula using statistical shape modeling. Journal of Orthopaedic Research, 38(10), pp. 2272-2279, 2020.

Matthijs Jacxsens, Shireen Y. Elhabian, Sarah Brady, Peter Chalmers, Robert Tashjian, Heath Henninger. Coracoacromial Morphology: A Contributor to Recurrent Traumatic Anterior Glenohumeral Instability?. Journal of Shoulder and Elbow Surgery, 28(7), pp. 1316-1325, 2019.

Sultana Sharmin, Praful Agrawal, Shireen Y. Elhabian, Ross Whitaker, Jason E. Blatt, Benjamin Gilles, Justin Cetas, Tanweer Rashid, Michel A. Audette. Medial Axis Segmentation of Cranial Nerves Using Shape Statistics-aware Discrete Deformable Models. International Journal of Computer Assisted Radiology and Surgery, pp. 1-13, 2019.

Penny R. Atkins, YongJae Shin, Praful Agrawal, Shireen Y. Elhabian, Ross T. Whitaker, Jeffrey A. Weiss, Stephen Kenji Aoki, Christopher L. Peters, and Anderson, Andrew. Which Two-dimensional Radiographic Measurements of Cam Femoroacetabular Impingement Best Describe the Three-dimensional Shape of the Proximal Femur?. Clinical Orthopaedics and Related Research, 477(1), pp. 242-253, 2019.

Liyun Tu, Martin Styner, Jared Vicory, Shireen Y. Elhabian, Rui Wang, Junpyo Hong, Beatriz Paniagua, Juan Carlos Prieto, Dan Yang, Ross Whitaker, Stephen Pizer. Skeletal Shape Correspondence through Entropy. IEEE Transactions on Medical Imaging. 37(1): pp. 1-11, 2018.

Gopalkrishna Veni, Shireen Y. Elhabian, and Ross T. Whitaker. ShapeCut: Bayesian Surface Estimation Using Shape-Driven Graph. Medical Image Analysis (2017).

Penny R. Atkins, Shireen Y. Elhabian, Praful Agrawal, Michael D. Harris, Ross T. Whitaker, Jeffrey A. Weiss, Christopher L. Peters, Andrew E. Anderson. Quantitative Comparison of Cortical Bone Thickness Using Correspondence-based Shape Modeling in Patients With Cam Femoroacetabular Impingement. Journal of Orthopaedic Research (2016).

Tu, Liyun, Jared Vicory, Shireen Y. Elhabian, Beatriz Paniagua, Juan Carlos Prieto, James N. Damon, Ross Whitaker, Martin Styner, Stephen M. Pizer. Entropy-based Correspondence Improvement of Interpolated Skeletal Models. Computer Vision and Image Understanding, 151 (2016): 72-79.

Shireen Y. Elhabian and Aly A. Farag. Helmholtz HSH-based Basis: A Compact Phenomenological Representation of Arbitrary Reflectance, Informatica. 2016 Mar 7;26(4): 593-620.

Shireen Y. Elhabian, Yaniv Gur, Clement Vachet, Joseph Piven, Martin Styner, Ilana Leppert, G. Bruce Pike, Guido Gerig. Subject-Motion Correction in HARDI Acquisitions: Choices and Consequences. Frontiers in Neurology, 5 (2014): 240.

Shireen Y. Elhabian and Aly A. Farag. Appearance-based Approach for Complete Human Jaw Shape Reconstruction. IET Computer Vision, 8(5), (2014): 404-418.

Shireen Y. Elhabian and Aly A. Farag. Image Irradiance Harmonics: A Phenomenological Model of Image Irradiance of Arbitrary Surface Reflectance. IET-Computer Vision, 8(5), (2014): 365-381.

Aly S. Abdelrahim, Aly A. Farag, Shireen Y. Elhabian, Moumen T. El-Melegy. Shape-from-Shading Using Sensor and Physical Object Characteristics Applied to Human Teeth Surface Reconstruction. IET Computer Vision, 8(1), (2014): 1-15.

Shireen Y. Elhabian and Aly A. Farag. Towards Efficient Image Irradiance Modelling of Convex Lambertian Surfaces Under Single Viewpoint and Frontal Illumination. IET Computer Vision, 7(6) (2013): 478-487.

Shireen Y. Elhabian, Khaled M. ElSayed, Sanaa ElOla H. Ahmed. Moving Object Detection in Spatial Domain using Background Removal Techniques - State-of-Art. Recent Patents on Computer Science, 1(1), (2008): 32-54.

Shireen Y. Elhabian, Khaled M. ElSayed, Sanaa ElOla H. Ahmed. Sperm Tracking using Backward Projection. Egyptian Informatics Journal, (2006).

Shireen Y. Elhabian, Khaled M. ElSayed, Sanaa ElOla H. Ahmed. Innovated Approach for Automated Snakes Initialization. Egyptian Informatics Journal, 5(1) (2004): 103-115.

Peer Reviewed Conference Proceedings

Deep Learning

Surojit Saha, Shireen Elhabian, Ross T. Whitaker. GENs: Generative Encoding Networks. European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), 2022, in press.

Jadie Adams, Shireen Y. Elhabian. From Images to Probabilistic Anatomical Shapes: A Deep Variational Bottleneck Approach. International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). Springer, Cham, 2022 (early accept).

Alessandro Ferrero, Shireen Y. Elhabian, Ross Whitaker. SetGANs: Enforcing Distributional Accuracy in Generative Adversarial Networks. The 25th International Conference on Image Processing, Computer Vision, and Pattern Recognition (IPCV), 2021.

Riddhish Bhalodia, Iain Lee, Shireen Y. Elhabian. dpVAEs: Fixing Sample Generation for Regularized VAEs. The 15th Asian Conference on Computer Vision (ACCV), 2020.

Hong Xu, David E. Timm, Shireen Y. Elhabian. Attention-Guided Quality Assessment for Automated Cryo-EM Grid Screening. The 23rd International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Springer, Cham, pp. 56-65, 2020. MICCAI 2020 NIH Award.

Riddhish Bhalodia, Shireen Y. Elhabian, Ladislav Kavan, Ross T. Whitaker. A Cooperative Autoencoder for Population-Based Regularization of CNN Image Registration. The 22nd International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pp. 391-400, 2019.

Riddhish Bhalodia, Anupama Goparaju, Alan Morris, Evgueni Kholmovski, Nassir Marrouche, Joshua Cates, Ross Whitaker, and Shireen Y. Elhabian. Deep Learning for End-to-End Atrial Fibrillation Recurrence Estimation. Computing in Cardiology (CinC), 2018.

Praful Agrawal, Ross T. Whitaker, Shireen Y. Elhabian. Learning Deep Features for Automated Placement of Correspondence Points on Ensembles of Complex Shapes. 20th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2017.

Shape Modeling

Alan Morris, Eugene Kholmovski, Nassir Marrouche, Joshua Cates, Shireen Y. Elhabian. An Image-based Approach for 3D Left Atrium Functional Measurements . IEEE Computing in Cardiology (CinC), 2020.

Ashley E. Morgan, Atefeh Kashani, Brian Zenger, Lindsay C Rupp, Maura D Perez, Markus D Foote, Alan K Morris, Mark B Ratcliffe, Jiwon J Kim, Jonathan W Weinsaft, Vikas Sharma, Rob S MacLeod, Shireen Y. Elhabian. Right Ventricular Shape Distortion in Tricuspid Regurgitation. IEEE Computing in Cardiology (CinC), 2020.

Wei Xing, Shireen Y. Elhabian, Ross Whitaker, Mike Kirby, Shandian Zhe. Infinite ShapeOdds: A Nonlinear Generative Model for Grid-Structured Shapes. The 34th AAAI Conference on Artificial Intelligence (AAAI), 2020.

Riddhish Bhalodia, Archanasri Subramanian, Alan, Morris, Joshua Cates, Ross Whitaker, Evgueni Kholmovski, Nassir Marrouche, Shireen Y. Elhabian. Does Alignment in Statistical Shape Modeling of Left Atrium Appendage Impact Stroke Prediction? Computing in Cardiology (CinC), 2019.

Anupama Goparaju, Alan Morris, Ibolya Csecs, Riddhish Bhalodia, Tom Ditter, Kristine Fuimaono, Evgueni Kholmovski, Nassir Marrouche, Joshua Cates, Shireen Y. Elhabian. Interatrial Septum and Appendage Ostium in Atrial Fibrillation Patients: A Population Study. Computing in Cardiology (CinC), 2019.

Shalin Parikh, Anupama Goparaju, Riddhish Bhalodia, Bosten Loveless, Alan Morris, Joshua Cates, Eugueni Kholmovski, Nassir Marrouche, Shireen Y. Elhabian. Efficient Segmentation Pipeline using Diffeomorphic Image Registration: A Validation Study. Computing in Cardiology (CinC), 2019.

Tim Sodergren, Anupama Goparaju, Alan Morris, Evgueni Kholmovski, Nassir Marrouche, Joshua Cates, and Shireen Y. Elhabian. Interactive Exploration of Left Atrium Population-Level Morphology in Atrial Fibrillation Patients. Computing in Cardiology (CinC), 2018.

Shireen Y. Elhabian and Ross T. Whitaker. ShapeOdds: Variational Bayesian Learning of Generative Shape Models. IEEE Conference on Computer Vision and Pattern Recognition (CVPR), pp. 2231-2242, 2017.

Shireen Y. Elhabian and Ross T. Whitaker. From Label Maps to Generative Shape Models: A Variational Bayesian Learning Approach. In International Conference on Information Processing in Medical Imaging (IPMI), pp. 93-105, 2017.

Shireen Y. Elhabian, Praful Agrawal, Ross Whitaker. Optimal Parameter Map Estimation for Shape Representation: A Generative Approach. In IEEE 13th International Symposium of Biomedical Imaging (ISBI), 2016.

Penny Atkins, Praful Agrawal, Shireen Y. Elhabian, Ross Whitaker, Jeffrey Weiss, Christopher Peters, Stephen Aoki, Andrew Anderson. Which Radiographic Measurements Best Identify Anatomical Variation In Femoral Head Anatomy? Analysis Using 3D Computed Tomography and Statistical Shape Modeling. Abstract for podium presentation at Annual Scientific Meeting of International Society of Hip Arthroscopy, 2016, San Francisco, CA.

Andrew Anderson, Penny R. Atkins, Praful Agrawal, Shireen Y. Elhabian, Ross T. Whitaker, Jeffrey A. Weiss, Christopher L. Peters, Stephen Kenji Aoki. Which Radiographic Measurements Best Identify Anatomical Variation in Femoral Head Anatomy? Analysis Using 3D Computed Tomography and Statistical Shape Modeling. Journal of Hip Preservation Surgery, 3, suppl 1 (2016).

Ahmed Farag, Shireen Y. Elhabian, Mostafa Abdelrahman, James Graham, Aly Farag, Dongqing Chen, Manuel F. Casanova. Surface Modeling of the Corpus Callosum from MRI Scans. Proc. of International Symposium on Visual Computing (ISVC), pp. 9-18, 2010.

Ahmed Farag, Shireen Y. Elhabian, Mostafa Abdelrahman, James Graham, Aly Farag, Dongqing Chen, Manuel F. Casanova. Shape Modeling of the Corpus Callosum. Proc. of the 32nd IEEE Engineering in Medicine and Biology Society (EMBC), pp. 4288-4291, 2010.

3D Shape Reconstruction

Eslam Mostafa, Shireen Y. Elhabian, Aly Abdelrahim, Salwa Elshazly and Aly Farag. Statistical morphable model for human teeth restoration. In IEEE International Conference on Image Processing (ICIP), pp. 4285-4288, 2014.

Aly Farag, Shireen Y. Elhabian, Aly Abdelrahim, Wael Aboelmaaty, Allan Farman and David Tazman. Model-based Human Teeth Shape Recovery from a Single Optical Image with Unknown Illumination. In Medical Computer Vision. Recognition Techniques and Applications in Medical Imaging, pp. 263-272. Springer Berlin Heidelberg, 2013.

Aly Abdelrahim, Ahmed Shalaby, Shireen Y. Elhabian, James Graham and Aly Farag. A 3D Reconstruction of the Human Jaw from a Single Image. 20th IEEE International Conference of Image Processing (ICIP), pp. 3622-3626, 2013.

Aly Abdelrahim, Aly Farag, Shireen Y. Elhabian, Eslam Mostafa and Wael Aboelmaaty. Occlusal Surface Reconstruction of Human Teeth from a Single Image Based on Object and Sensor Physical Characteristics. In Image Processing (ICIP), 2012 19th IEEE International Conference on, pp. 1793-1796. IEEE, 2012.

Shireen Y. Elhabian, Aly Abdelrahim, Aly Farag, David Tasman, Wael Aboelmaaty, Allan Farman. Clinical Crowns Shape Reconstruction - an Image-based Approach. IEEE 10th International Symposium on Biomedical Imaging (ISBI), pp. 93-96. IEEE, 2013.

Shireen Y. Elhabian, Eslam Mostafa, Ham Rara, Aly Farag. Non-Lambertian Model-based Facial Shape Recovery from Single Image Under Unknown General Illumination. Ninth Canadian Conference on Computer and Robot Vision (CRV), pp. 252-259. IEEE, 2012.

Shireen Y. Elhabian, Ham Rara, Asem Ali, Aly Farag. Illumination-invariant Statistical Shape Recovery with Contiguous Occlusion. Eighth Canadian Conference on Computer and Robot Vision (CRV), pp. 301-308, 2011.

Ham Rara, Shireen Y. Elhabian, Thomas Starr, Aly Farag. 3D Face Recovery from Intensities of General and Unknown Lightning Using Partial Least Squares. Proc. of 2010 IEEE International Conference on Image Processing (ICIP), pp. 4041-4044, 2010

Ham Rara, Shireen Y. Elhabian, Thomas Starr, Aly Farag. Model-Based Shape Recovery from Single Images of General and Unknown Lighting. IEEE International Conference on Image Processing (ICIP), Nov. 7 - Nov. 10, 2009, pp. 517-520.

Ham Rara, Shireen Y. Elhabian, Thomas Starr, Aly Farag. Face Reconstruction and Recognition Using a Statistical Model Combining Shape and Spherical Harmonics. IEEE SOUTHEASTCON, March 2009, pp. 350-355.

Ham Rara, Shireen Y. Elhabian, Thomas Starr, Aly Farag. A Statistical Model Combining Shape and Spherical Harmonics for Face Reconstruction and Recognition. Biomedical Engineering Conference, CIBEC2008. Cairo International, 1:1-4, 18-20 Dec. 2008.

Amal Farag, Shireen Y. Elhabian, Abdelrehim Ahmed, Aly Farag. Noise Analysis of a SFS Algorithm Formulated under Various Imaging Conditions. 4th International Symposium on Visual Computing, December 1-3, 2008, Las Vegas, Nevada, USA. pp. 793-802.

Image Segmentation

Gopalkrishna Veni, Shireen Y. Elhabian, Ross Whitaker. A Bayesian Formulation of Graph-Cut Surface Estimation With Global Shape Priors. In IEEE 12th International Symposium on Biomedical Imaging (ISBI), 2015, pp. 368-371.

Marwa Ismail, Shireen Y. Elhabian, Aly Farag, Gerald Dryden, Albert Seow. 3D Automated Colon Segmentation for Efficient Polyp Detection. In Biomedical Engineering Conference (CIBEC), 2012 Cairo International, pp. 48-51. IEEE, 2012.

Diffusion Imaging

Shireen Y. Elhabian, Clement Vachet, Joseph Piven, Martin Styner, Guido Gerig. Compressive Sensing-based Q-space Resampling for Handling Fast Bulk Motion in HARDI Acquisitions. In IEEE 13th International Symposium of Biomedical Imaging (ISBI), 2016.

Shireen Y. Elhabian, Yaniv Gur, Clement Vachet, Joseph Piven, Martin Styner, Ilana Leppert, G. Bruce Pike, Guido Gerig. A Preliminary Study on the Effect of Motion Correction On HARDI Reconstruction. In Proceedings of the 2014 IEEE International Symposium on Biomedical Imaging (ISBI), 2014, pp. 1055-1058.

Appearance Modeling

Shireen Y. Elhabian and Aly Farag. Analytic Bilinear Appearance Subspace Construction for Modeling Image Irradiance under Natural Illumination and Non-Lambertian Reflectance. In Computer Vision and Pattern Recognition (CVPR), 2013 IEEE Conference on, pp. 1446-1451. IEEE, 2013.

Shireen Y. Elhabian and Aly Farag. Modeling Image Irradiance under Natural Illumination and Isotropic Surface Reflectance. 19th IEEE International Conference on Image Processing (ICIP), pp. 3013-3016. IEEE, 2012.

Shireen Y. Elhabian, Ham Rara and Aly Farag. Towards Efficient and Compact Phenomenological Representation of Arbitrary Bidirectional Surface Reflectance. British Machine Vision Conference (BMVC), vol. 89, pp 1-11, Aug 2011.

Shireen Y. Elhabian, Ham Rara and Aly Farag. Towards Accurate and Efficient Representation of Image Irradiance of Convex-Lambertian Objects under Unknown Near Lighting. International Conference of Computer Vision (ICCV), pp. 1732 - 1737, Nov 2011.

Shireen Y. Elhabian, Ham Rara, Aly Farag. Modeling Lambertian Surfaces under Unknown Distant Illumination Using Hemispherical Harmonics. Eighth Canadian Conference on Computer and Robot Vision (CRV), pp.293-300, 2011.

Shireen Y. Elhabian, Ham Rara and Aly Farag. On The Use of Hemispherical Harmonics for Modeling Images of Object under Known Distant Illumination. International Conference of Image Processing (ICIP), pp. 1109 - 1112, Sept 2011.

Biometrics

Mostafa Abdelrahman, Shireen Y. Elhabian, Asem Ali and Aly A. Farag. Face Recognition at-a-Distance Using Texture, Sparse-Stereo, Dense-Stereo, Inteprnational Conference on Multimedia Technology (ICMT), pp. 6690-6695, 26-28 July 2011.

Ham Rara, Aly Farag, Shireen Y. Elhabian, Asem Ali, Mike Miller, Thomas Starr, Todd Davis. Face Recognition at-a-Distance Using Texture and Sparse-Stereo Reconstruction. Proc. of IEEE Fourth International Conference on Biometrics: Theory, Applications and Systems (BTAS), pp. 1221-1224, 2010.

Ham Rara, Asem Ali, Shireen Y. Elhabian, Thomas Starr, Aly A. Farag. Face Recognition at-a-Distance Using Texture, Dense- and Sparse-Stereo Reconstruction. Proceedings of the International Conference on Pattern Recognition (ICPR), pp. 1221-1224, 2010.

Ham Rara, Shireen Y. Elhabian, Asem Ali, Travis Gault, Mike Miller, Thomas Starr, Aly Farag. A Framework for Long Distance Face Recognition Using Dense- and Sparse-Stereo Reconstruction. 5th International Symposium on Visual Computing (ISVC09), Nov. 30 - Dec. 2, 2009, Las Vegas, Nevada, USA. , pp. 774-783.

Ham Rara, Shireen Y. Elhabian, Asem Ali, Mike Miller, Thomas Starr, Aly Farag. Distant Face Recognition Based on Sparse Stereo Reconstruction. IEEE International Conference on Image Processing (ICIP), Nov. 7 - Nov. 10, 2009, pp. 4141-4144.

Pattern Recognition

Amal A. Farag, Asem M. Ali, Shireen Y. Elhabian and Aly A. Farag. Probability Density Estimation By Linear Combinations Of Gaussian Kernels: Generalizations and Algorithmic Evaluation. International Conference on Multimedia Technology (ICMT), pp. 6491-6494, 26-28 July 2011.

Mostafa Abdelrahman, Asem Ali, Shireen Y. Elhabian and Aly Farag. Solving Geometric Co-Registration Problem of Multi-Spectral Remote Sensing Imagery Using SIFT-based Features Toward Precise Change Detection. 7th International Symposium on Visual Computing (ISVC). Las Vegas, Nevada, USA, September 26-28, 2011, vol.2, pp 607-616.

Amal Farag, Asem Ali, Shireen Y. Elhabian, James Graham, Aly Farag, Robert Falk. Feature-Based Lung Nodule Classification. Proc. of International Symposium on Visual Computing (ISVC), pp. 79-88, 2010.

Amal Farag, Shireen Y. Elhabian, James Graham, Aly Farag, Robert Falk. Toward Precise Pulmonary Nodule Descriptors for Nodule Type Classification. Proc. of the 13th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pp. 626-633, 2010.

Amal Farag, Shireen Y. Elhabian, James Graham, Aly Farag, Salwa Elshazly, Robert Falk, Hani Mahdi, Hossam Abdelmunim, Sahar Al-Ghaafary. Modeling of the Lung Nodules for Detection in LDCT Scans. Proc. of the 32nd IEEE Engineering in Medicine and Biology Society (EMBC), 2010, pp. 3618-3621.

Shireen Y. Elhabian, Amal Farag, Salwa Elshazly, Aly Farag. Sensitivity of Template Matching for Pulmonary Nodule Detection: A Case Study. In IEEE Biomedical Engineering Conference (CIBEC). Cairo International, pp. 1-4, 2008.

Shireen Y. Elhabian, Hossam Abd EL Munim, Salwa Elshazly, Aly A Farag, Mohamed Aboelghar. Experiments on Sensitivity of Template Matching for Lung Nodule Detection in Low Dose CT Scans. IEEE International Symposium on Signal Processing and Information Technology (ISSPIT) 2007, 1040-1046.

Workshops

Jadie Adams, Nawazish Khan, Alan Morris, Shireen Y. Elhabian. [Spatiotemporal Cardiac Statistical Shape Modeling: A Data-Driven Approach]. MICCAI-STACOM 2022.

Krithika Iyer, Alan Morris, Brian Zenger, Karthik Karanth, Oleksandre Korshak, Shireen Y. Elhabian. Statistical Shape Modeling of Biventricular Anatomy with Shared Boundaries. MICCAI- STACOM 2022.

Jadie Adams, Riddhish Bhalodia, Shireen Y. Elhabian. Uncertain-DeepSSM: From Images to Probabilistic Shape Models. In MICCAI: International Workshop on Shape in Medical Imaging, Springer, Cham., pp. 57-72, 2020. ShapeMI Runner-Up Paper Award - 2nd place

Praful Agrawal, Joseph Mozingo, Shireen Y. Elhabian, Andrew E. Anderson, Ross Whitaker. Combined Estimation of Shape and Pose for Statistical Analysis of Articulating Joints. In MICCAI: International Workshop on Shape in Medical Imaging, Springer, Cham., pp. 111-121, 2020.

Riddhish Bhalodia, Shireen Y. Elhabian, Ladislav Kavan, and Ross T. Whitaker. DeepSSM: A Deep Learning Framework for Statistical Shape Modeling from Raw Images. ShapeMI-MICCAI 2018: Workshop on Shape in Medical Imaging, 2018.

Anupama Goparaju, Ibolya Csecs, Alan Morris, Evgueni Kholmovski, Nassir Marrouche, Ross T. Whitaker, and Shireen Y. Elhabian. On the Evaluation and Validation of Off-the-shelf Statistical Shape Modeling Tools: A Clinical Application. ShapeMI-MICCAI 2018: Workshop on Shape in Medical Imaging, 2018.

Tim Sodergren, Riddhish Bhalodia, Ross Whitaker, Joshua Cates, Nassir Marrouche, and Shireen Y. Elhabian. Mixture Modeling of Global Shape Priors and Autoencoding Local Intensity Priors for Left Atrium Segmentation. STACOM-MICCAI: Statistical Atlases and Computational Modeling of the Heart workshop, 2018.

Sultana, Sharmin, Praful Agrawal, Shireen Y. Elhabian, Ross T. Whitaker, Tanweer Rashid, Jason E. Blatt, Justin S. Cetas, Michel A. Audette. Towards a Statistical Shape-Aware Deformable Contour Model for Cranial Nerve Identification. In Workshop on Clinical Image-Based Procedures, Springer International Publishing, pp. 68-76, 2016.

Shireen Y. Elhabian, Yaniv Gur, Clement Vachet, Joseph Piven, Martin Styner, Ilana Leppert, G. Bruce Pike, Guido Gerig. Motion is Inevitable: The Impact of Motion Correction Schemes on HARDI Reconstructions. MICCAI 2014 Workshop on Computational Diffusion MRI (CDMRI) 2014. pp. 169-179.

Marwa Ismail, Shireen Y. Elhabian, Aly Farag and Gerald W. Dryden. Fully Automated 3D Colon Segmentation for Early Detection of Colorectal Cancer Based on Convex Formulation of the Active Contour Model. IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshop (CVPRW), pp. 58-63. IEEE, 2012.

Mostafa Abdelrahman, Asem Ali, Shireen Y. Elhabian, Ham Rara, Aly A. Farag. A Passive Stereo System for 3D Human Face Reconstruction and Recognition at a Distance. IEEE CVPR Workshop on Biometrics, 2012, pp. 17-22.

Ham Rara, Shireen Y. Elhabian, Asem Ali, Mike Miller, Thomas Starr, Aly Farag. Face Recognition at a Distance Based on Sparse-Stereo Reconstruction. IEEE CVPR Biometrics Workshop, 2009, pp. 27-32.

Amal Farag, Shireen Y. Elhabian, Salwa Elshazly, Aly Farag. Quantification of nodule detection in chest CT: A clinical investigation based on the ELCAP study. In Proceeding of Second International Workshop on Pulmonary Image Processing in conjunction with MICCAI, pp. 149-160, 2009.

Abstracts

Penny R. Atkins, Shireen Y. Elhabian, Jeffrey A. Weiss, Ross T. Whitaker, Christopher L. Peters, Andrew E. Anderson. Combination of Statistical Shape Modeling and Statistical Parametric Mapping to Quantify Cartilage Contact Mechanics in Hip Dysplasia. PanaSoMM 2022 Abstract.

Penny R. Atkins, Praful Agrawal, Joseph D. Mozingo, Keisuke Uemura, Kunihiko Tokunaga, Christopher L. Peters, Shireen Y. Elhabian, Ross T. Whitaker, Andrew E. Anderson. Use of Statistical Shape Modeling to Predict Clinical Metrics of Femoral Head Coverage in Patients with Developmental Dysplasia. PanaSoMM 2022 Abstract.

Penny R. Atkins, Shireen Y. Elhabian, Jeffrey A. Weiss, Ross T. Whitaker, Christopher L. Peters, Andrew E. Anderson. Quantification of Cartilage Mechanics through Statistical Shape Modeling and Statistical Parametric Mapping. Orthopedics Research Society, 2022.

Penny R. Atkins, Praful Agrawal, Joseph D. Mozingo, Keisuke Uemura, Kunihiko Tokunaga, Christopher L. Peters, Shireen Y. Elhabian, Ross T. Whitaker, Andrew E. Anderson. Prediction of Clinical Measures of Femoral Head Coverage from Statistical Shape Modeling Parameters in Patients with Developmental Dysplasia. Orthopedics Research Society (podium presentation), 2022.

Andrew C. Peterson, Rich J. Lisonbee, Nicola Krahenbuhl, Charles L. Saltzman, Andrew E. Anderson, Alexej Barg, Shireen Elhabian, Amy L. Lenz. Multi-Domain Statistical Shape Model of the Subtalar, Talonavicular and Calcaneocuboid Joints. Orthopedics Research Society, 2022.

Joseph D. Mozingo, Penny R. Atkins, Praful Agrawal, Keisuke Uemura, Shireen Y. Elhabian, Ross T. Whitaker, Andrew E. Anderson. Morphology of Hip Dysplasia in Japanese Females: A Statistical Shape Modeling Study. American Society of Biomechanics (ASB) Conference, 2021.

Matthijs Jacxsens, Shireen Y. Elhabian, Peter N. Chalmers, Robert Z. Tashjian, Heath B. Henninger. Thinking Outside the Glenohumeral Box: Hierarchical Shape Variation of the Periarticular Anatomy of the Scapula Using Statistical Shape Modeling. Anatomy and Biomechanics at International Congress of Shoulder and Elbow Therapist (ICSES), 2019.

Matthijs Jacxsens, Shireen Y. Elhabian, Robert Z. Tashjian, Heath B. Henninger. Periarticular and Glenoid Morphology of the Scapular Differs in Patients with Hill-Sachs Lesions: a Controlled Statistical Shape Modeling Study. 78th Annual Conference of the Swiss Society of Orthopedics and Trauma Surgery, 6-8th June 2018, Montreux, Switzerland

Matthijs Jacxsens, Shireen Y. Elhabian, Robert Z. Tashjian, Heath B. Henninger. Scapular Morphology In Patients With Hill-Sachs Lesions Using Statistical Shape Modeling. Abstract for podium presentation for the 27th Congress of the European Society for Surgery of the Shoulder and the Elbow (SECEC-ESSSE) conference, 2017.

Penny Atkins, Stephen Aoki, Shireen Y. Elhabian, Praful Agrawal, Ross Whitaker, Jeffrey Weiss, Christopher Peters, Andrew Anderson. Evaluation of the Sclerotic Subchondral Bone Boundary as a Surgical Resection Guide in the Treatment of Cam-type Femoroacetabular Impingement. Annual Meeting of Orthopaedic Research Society, 2017.

Penny Atkins, Praful Agrawal, Shireen Y. Elhabian, Ross Whitaker, Jeffrey Weiss, Christopher Peters, Stephen Aoki, Andrew Anderson. Which Radiographic Measurements Best Identify Anatomical Variation In Femoral Head Anatomy? Analysis Using 3D Computed Tomography and Statistical Shape Modeling. Abstract for podium presentation at Annual Scientific Meeting of International Society of Hip Arthroscopy, San Francisco, CA, 2016.

Penny Atkins, Prateep Mukherjee, Shireen Y. Elhabian, Sumedha Singla, Michael Harris, Ross Whitaker, Jeffrey Weiss, Andrew Anderson. Warping of Template Meshes for Efficient Subject Specific FE Mesh Generation. Abstract for podium presentation, International Symposium on Computer Methods in Biomechanics and Biomedical Engineering, 2015. Montreal, Canada.

Penny Atkins, Prateep Mukherjee, Shireen Y. Elhabian, Sumedha Singla, Michael Harris, Jeffrey Weiss, Ross Whitaker, Andrew Anderson. Proximal Femoral Cortical Bone Thickness in Patients with Femoroacetabular Impingement and Normal Hips Analyzed Using Statistical Shape Modeling. Abstract for podium presentation, Summer Biomechanics, Bioengineering and Biotransport Conference, 2015, Snowbird, UT.

Penny Atkins, Prateep Mukherjee, Sumedha Singla, Shireen Y. Elhabian, Michael Harris, Jeffrey Weiss, Ross Whitaker, Andrew Anderson. Statistical Shape Modeling to Quantify and Comparison of Proximal Femoral Cortical Bone Thickness between Patients with Femoroacetabular Impingement and Normal Hips Analyzed by Statistical Shape Modeling. Abstract for podium presentation, Orthopaedic Research Society, 2015, Las Vegas, NV.

Penny Atkins, Prateep Mukherjee, Sumedha Singla, Shireen Y. Elhabian, Michael Harris, Jeffrey Weiss, Ross Whitaker, Andrew Anderson. Statistical Shape Modeling of Cortical Bone Thickness in Patients with Femoroacetabular Impingement. Abstract for podium presentation. Biomedical Engineering Society, 2014, San Antonio, TX.

Shireen Y. Elhabian, Yaniv Gur, Joseph Piven, Martin Styner, Ilana Leppert, G. Bruce Pike, Guido Gerig. Subject-Motion Correction in HARDI Acquisitions: Choices and Consequences. In Proceeding of the 2014 Joint Annual Meeting ISMRM-ESMRMB, 2014.

Preprints

Krithika Iyer, Riddhish Bhalodia, Shireen Y. Elhabian. RENs: Relevance Encoding Networks. arXiv:2205.13061, 2022 (under review - Neural Information Processing Systems (NeurIPS))

Wenzheng Tao, Riddhish Bhalodia, Shireen Y. Elhabian. Learning Population-level Shape Statistics and Anatomy Segmentation From Images: A Joint Deep Learning Model. arXiv:2201.03481, 2022.

Riddhish Bhalodia, Shireen Y. Elhabian, Jadie Adams, Wenzheng Tao, Ladislav Kavan, Ross T. Whitaker. DeepSSM: A Blueprint for Image to Shape Deep Learning Models. arXiv preprint arXiv:2110.07152, 2021 (under review - Medical Imaging Analysis).

Praful Agrawal, Ross Whitaker, Shireen Y. Elhabian. Learning Deep Features for Shape Correspondence with Domain Invariance. arXiv preprint arXiv:2102.10493, 2021

Daniel Perry, Vahid Keshavarzzadeh, Shireen Elhabian, Robert Kirby, Michael Gleicher, Ross Whitaker. Visualization of topology optimization designs with representative subset selection. arXiv preprint arXiv:2012.14901. December 2020.

Riddhish Bhalodia, Shireen Y. Elhabian, Ladislav Kavan, Ross Whitaker. CoopSubNet: Cooperating Subnetwork for Data-Driven Regularization of Deep Networks under Limited Training Budgets. arXiv:1906.05441, 2019.

Yen Yun Yu, Shireen Y. Elhabian, Ross T. Whitaker. Clustering with Pairwise Relationships: A Generative Approach. arXiv:1805.02285, 2018.

Technical Reports

Shireen Y. Elhabian, Praful Agrawal, Joshua Cates, Manasi Datar, Ross Whitaker. ShapeWorksStudio: Particle-based Shape Correspondence and Visualization Software. Technical Report. Scientific Computing and Imaging Institute, University of Utah, July 2017

Shireen Y. Elhabian and Aly Farag. A Flavor of Computational Geometry: Voronoi Diagrams. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, March 2010.

Shireen Y. Elhabian and Aly Farag. A Flavor of Computational Geometry: Convex Hull. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, February 2010.

Shireen Y. Elhabian and Aly Farag. A Flavor of Computational Geometry: Polygon Triangulation. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, February 2010.

Shireen Y. Elhabian and Aly Farag. A Tutorial on Curves and Surfaces. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, February 2010.

Shireen Y. Elhabian and Aly Farag. A Flavor of Topology. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, January 2010.

Shireen Y. Elhabian. A Tutorial on Iris Recognition. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, November 2009.

Shireen Y. Elhabian and Aly Farag. 2D Face Recognition Using PCA, ICA and LDA. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, October 2009.

Shireen Y. Elhabian and Aly Farag. A Tutorial on Data Reduction: Principal Component Analysis Theoretical Discussion. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, September 2009.

Shireen Y. Elhabian and Aly Farag. A Tutorial on Data Reduction: Linear Discriminant Analysis. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, September 2009.

Shireen Y. Elhabian and Aly Farag. A Tutorial on Data Reduction: Independent Component Analysis. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, September 2009.

Shireen Y. Elhabian and Aly Farag. Exploring the Interplay between Facial 3D Reconstruction and Recognition. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, August 2009.

Shireen Y. Elhabian and Aly Farag. Tutorial on Computational Geometry. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, July 2009.

Shireen Y. Elhabian, Amal Farag and Aly Farag. Tutorial on Rigid Registration: Iterative Closest Point. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, March 2009.

Shireen Y. Elhabian and Aly Farag. Tutorial on MRI Reconstructions. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, February 2009.

Shireen Y. Elhabian, Amal Farag and Aly Farag. Tutorial on CT Reconstructions. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, January 2009.

Shireen Y. Elhabian. Hands on Shape from Shading. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, April 2008.

Shireen Y. Elhabian and Aly Farag. Tutorial on Stereo Reconstruction. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, March 2008.

Shireen Y. Elhabian. Tutorial on Camera Calibration. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, February 2008.

Shireen Y. Elhabian and Aly Farag. Hands-on Generating Random Numbers. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, October 2007.

Shireen Y. Elhabian and Aly Farag. Biometrics in a glimpse. Technical Report. Computer Vision and Image Processing Laboratory, CVIP Lab, University of Louisville, September 2007.

Dissertation

Shireen Y. Elhabian. Phenomenological Modeling of Image Irradiance for Non-Lambertian Surfaces under Natural Illumination. PhD dissertation. University of Louisville, Louisville, KY, USA, 2012.