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The following selected papers give background on the methods used in ShapeWorks, and a sample of the areas ShapeWorks has been applied:
M. Jacxsens, S. Elhabian, S. Brady, P. Chalmers, R. Tashjian, and H. Henninger. "Coracoacromial morphology: a contributor to recurrent traumatic anterior glenohumeral instability," Journal of Shoulder and Elbow Surgery, 1:1316-1325, 2019.
P. R. Atkins, Y. Shin, P. Agrawal, S. Y. Elhabian, R. T. Whitaker, J. A. Weiss, S. K. Aoki, C. L. Peters ,and A. E. Anderson. "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):242–253, 2019.
T. Sodergren, R. Bhalodia, R. Whitaker, J. Cates, N. Marrouche, and S. Elhabian. "Mixture modeling of global shape priors and autoencoding local intensity priors for left atrium segmentation," In STACOM- MICCAI: Statistical Atlases and Computational Modeling of the Heart workshop, page in press. Springer, 2018.
A. Goparaju, I. Csecs, A. Morris, E. Kholmovski, N. Marrouche, R. Whitaker, and S. Elhabian. "On the Evaluation and Validation of Off-the-Shelf Statistical Shape Modeling Tools: A Clinical Application," In International Workshop on Shape in Medical Imaging, pages 14–27. Springer, 2018.
E. T. Bieging, A. Morris, B. D. Wilson, C. J. McGann, N. F. Marrouche, and J. Cates. "Left atrial shape predicts recurrence after atrial fibrillation catheter ablation," Journal of Cardiovascular Electrophysiology, 2018.
P. R. Atkins, S. Y. Elhabian, P. Agrawal, M. D. Harris, R. T. Whitaker, J. A. Weiss, C. L. Peters, and A. E. Anderson. "Quantitative comparison of cortical bone thickness using correspondence-based shape modeling in patients with cam femoroacetabular impingement," Journal of Orthopaedic Research, 35(8):1743–1753, 2017.
J. Cates, L. Nevell, S. I. Prajapati, L. D. Nelon, J. Y. Chang, M. E. Randolph, B. Wood, C. Keller, and R. T. Whitaker. "Shape analysis of the basioccipital bone in Pax7-deficient mice," Scientific Reports, 7(1):17955, 2017.
J. Cates, S. Elhabian, and R. Whitaker. "ShapeWorks: particle-based shape correspondence and visualization software," In G. Zheng, S. Li, and G. Szekely, editors, Statistical Shape and Deformation Analysis: Methods, Implementation and Applications, 1st Edition, chapter 10. Academic Press, 2017.
P. Agrawal, S.Y. Elhabian, R.T. Whitaker, "Learning Deep Features for Automated Placement of Correspondence Points on Ensembles of Complex Shapes," In International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 185-193. Springer, Cham, 2017.
S. Sultana, P. Agrawal, S. Elhabian, R. Whitaker, T. Rashid, J. Blatt, J. Cetas, and M. Audette. "Towards a statistical shape-aware deformable contour model for cranial nerve identification," In Workshop on Clinical Image-Based Procedures, pages 68–76. Springer, 2016.
J. Cates, E. Bieging, A. Morris, G. Gardner, N. Akoum, E. Kholmovski, N. Marrouche, C. McGann, and R. S. MacLeod. "Computational shape models characterize shape change of the left atrium in atrial fibrillation," Clinical Medicine Insights. Cardiology, 8(Suppl 1):99, 2015.
Ken Museth. "VDB: High-resolution sparse volumes with dynamic topology" ACM Transactions on Graphics, July 2013, Article No.: 27
M. Datar, I. Lyu, S. Kim, J. Cates, M. Styner, R. Whitaker. "Geodesic distances to landmarks for dense correspondence on ensembles of complex shapes," In International Conference on Medical Image Computing and Computer-Assisted Intervention, Springer, Berlin, Heidelberg, pp. 19-26, 2013.
M.D. Harris, M. Datar, R.T. Whitaker, E.R. Jurrus, C.L. Peters, A.E. Anderson. "Statistical Shape Modeling of Cam Femoroacetabular Impingement," In Journal of Orthopaedic Research, Vol. 31, No. 10, pp. 1620--1626. 2013.
K.B. Jones, M. Datar, S. Ravichandran, H. Jin, E. Jurrus, R.T. Whitaker, M.R. Capecchi. "Toward an Understanding of the Short Bone Phenotype Associated with Multiple Osteochondromas," In Journal of Orthopaedic Research, Vol. 31, No. 4, pp. 651--657. 2013.
J. Cates, P.T. Fletcher, Z. Warnock, R.T. Whitaker. "A Shape Analysis Framework for Small Animal Phenotyping with Application to Mice with a Targeted Disruption of Hoxd11," In Proceedings of the 5th IEEE International Symposium on Biomedical Imaging (ISBI '08), pp. 512--516. 2008. DOI: 10.1109/ISBI.2008.4541045
J. Cates, P.T. Fletcher, M. Styner, H. Hazlett, R.T. Whitaker. "Particle-Based Shape Analysis of Multi-Object Complexes," In Proceedings of the 11th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI '08), Lecture Notes In Computer Science (LCNS), pp. 477--485. 2008. ISBN: 978-3-540-85987-1
J. Cates, P. T. Fletcher, M. Styner, M. Shenton, and R. Whitaker. "Shape modeling and analysis with entropy-based particle systems," In Information Processing in Medical Imaging, pages 333–345. Springer, 2007.