[1] Q. Song, J. Bai, M. Garvin, M. Sonka, J. Buatti, X. Wu, et al.
, “Optimal multiple surface segmentation with shape and context priors,” IEEE Transactions on Medical Imaging , vol. 32, no. 2, pp. 376–386, 2013. 15545069.
[2] T. Shepherd, M. Teras, R. R. Beichel, R. Boellaard, M. Bruynooghe, V. Dicken, M. J. Gooding, P. J. Julyan, J. A. Lee,
S. Lefevre, M. Mix, V. Naranjo, X. Wu, H. Zaidi, Z. Zeng, and H. Minn, “Comparative study with new accuracy metrics for target volume contouring in PET image guided radiation therapy,” IEEE Transactions on Medical Imaging , vol. 31, pp. 2006–2024, Nov. 2012.
[3] X. Dou, Y. Kim, J. E. Bayouth, J. M. Buatti, and X. Wu, “Optimal field-splitting algorithm in intensity-modulated radiotherapy: Evaluations using head-and-neck and female pelvic IMRT cases,” In press, Medical Dosimetry , 2012.
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[4] D. Han, J. E. Bayouth, S. Bhatia, M. Sonka, and X. Wu, “Characterization and identification of spatial artifacts during
4D-CT imaging,” Medical Physics , vol. 38, pp. 2074–2087, Apr. 2011. PMC3078159.
[5] X. Wu, X. Dou, A. Wahle, and M. Sonka, “Region detection by minimizing intraclass variance with geometric constraints, global optimality, and efficient approximation,” IEEE Transactions on Medical Imaging , vol. 30, pp. 814–827,
Mar. 2011. PMC3131164.
[6] D. Han, M. Sonka, J. E. Bayouth, and X. Wu, “Optimal multiple-seams search for image resizing with smoothness and shape prior,” The Visual Computer , vol. 26, no. 6, pp. 749–759, 2010. http://dx.doi.org/10.1007/s00371-010-0480-8.
[7] X. Wu, “Efficient algorithms for the optimal-ratio region detection problems in discrete geometry with applications,” International Journal of Computational Geometry & Applications , vol. 19, pp. 141–159, Apr. 2009.
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[8] J. Bai, Q. Song, O. Veksler, and X. Wu, “Fast dynamic programming for labeling problems with ordering constraints,” in 2012 IEEE Conference on Computer Vision and Pattern Recognition (CVPR) , pp. 1728–1735, June 2012.
[9] L. Xu, B. Stojkovic, H. Ding, Q. Song, X. Wu, M. Sonka, and J. Xu, “Faster segmentation algorithm for optical coherence tomography images with guaranteed smoothness,” in Machine Learning in Medical Imaging (K. Suzuki,
F. Wang, D. Shen, and P. Yan, eds.), vol. 7009 of Lecture Notes in Computer Science , pp. 308–316, Springer Berlin /
Heidelberg, 2011.
[10] D. Han, J. Bayouth, Q. Song, S. Bhatia, M. Sonka, and X. Wu, “Feature guided motion artifact reduction with structureawareness in 4D CT images,” in 2011 IEEE Conference on Computer Vision and Pattern Recognition (CVPR) , pp. 1057–1064, June 2011. PMC3207360.
[11] Q. Song, M. Chen, J. Bai, M. Sonka, and X. Wu, “Surface–Region context in optimal multi-object Graph-Based segmentation: Robust delineation of pulmonary tumors,” in Information Processing in Medical Imaging (G. Szekely and H. Hahn, eds.), vol. 6801 of Lecture Notes in Computer Science , pp. 61–72, Springer Berlin / Heidelberg, 2011.
PMC3158678.
[12] L. Xu, B. Stojkovic, Y. Zhu, Q. Song, X. Wu, M. Sonka, and J. Xu, “Efficient algorithms for segmenting globally optimal and smooth multi-surfaces,” in Information Processing in Medical Imaging (G. Szekely and H. Hahn, eds.), vol. 6801 of Lecture Notes in Computer Science , pp. 208–220, Springer Berlin / Heidelberg, 2011. PMC3679538.
[13] D. Han, J. E. Bayouth, Q. Song, A. Taurani, M. Sonka, J. Buatti, and X. Wu, “Globally optimal tumor segmentation in
PET-CT images: A Graph-Based co-segmentation method,” in Information Processing in Medical Imaging (G. Szekely and H. Hahn, eds.), vol. 6801 of Lecture Notes in Computer Science , pp. 245–256, Springer Berlin / Heidelberg, 2011.
PMC3158679.
[14] D. Han, J. E. Bayouth, S. Bhatia, M. Sonka, and X. Wu, “Motion artifact reduction in 4D helical CT: Graph-Based structure alignment,” in Medical Computer Vision. Recognition Techniques and Applications in Medical Imaging (B. Menze,
G. Langs, Z. Tu, and A. Criminisi, eds.), vol. 6533 of Lecture Notes in Computer Science , pp. 63–73, Springer Berlin
/ Heidelberg, 2011.
[15] Q. Song, Y. Liu, Y. Liu, P. Saha, M. Sonka, and X. Wu, “Graph search with appearance and shape information for
3-D prostate and bladder segmentation,” in Medical Image Computing and Computer-Assisted Intervention– MICCAI
2010 (T. Jiang, N. Navab, J. Pluim, and M. Viergever, eds.), vol. 6363 of Lecture Notes in Computer Science , pp. 172–
180, Springer Berlin / Heidelberg, 2010. 20879397.
[16] Q. Song, X. Wu, Y. Liu, M. Sonka, and M. K. Garvin, “Simultaneous searching of globally optimal interacting surfaces with shape priors,” in 2010 IEEE Conference on Computer Vision and Pattern Recognition (CVPR) , pp. 2879–2886,
June 2010.

[17] D. Han, X. Wu, and M. Sonka, “Optimal multiple surfaces searching for video/image resizing - a graph-theoretic approach,” in 2009 IEEE 12th International Conference on Computer Vision , pp. 1026–1033, Oct. 2009.
[18] Q. Song, X. Wu, Y. Liu, M. Smith, J. Buatti, and M. Sonka, “Optimal graph search segmentation using arc-weighted graph for simultaneous surface detection of bladder and prostate,” in Medical Image Computing and Computer-
Assisted Intervention– MICCAI 2009 (G.-Z. Yang, D. Hawkes, D. Rueckert, A. Noble, and C. Taylor, eds.), vol. 5762 of Lecture Notes in Computer Science , pp. 827–835, Springer Berlin / Heidelberg, 2009. 20426188.
[19] M. Gibson, D. Han, M. Sonka, and X. Wu, “Maximum weight digital regions decomposable into digital Star-Shaped regions,” in Algorithms and Computation (T. Asano, S. Nakano, Y. Okamoto, and O. Watanabe, eds.), vol. 7074 of
Lecture Notes in Computer Science , pp. 724–733, Springer Berlin Heidelberg, 2011.
[20] A. Delong, L. Gorelick, F. Schmidt, O. Veksler, and Y. Boykov, “Interactive segmentation with super-labels,” in Energy
Minimization Methods in Computer Vision and Pattern Recognition (Y. Boykov, F. Kahl, V. Lempitsky, and F. Schmidt, eds.), vol. 6819 of Lecture Notes in Computer Science , pp. 147–162, Springer Berlin Heidelberg, 2011.
[21] Z. Hu, X. Wu, A. Hariri, and S. R. Sadda, “Multiple layer segmentation and analysis in three-dimensional spectraldomain optical coherence tomography volume scans,” Journal of Biomedical Optics , vol. 18, no. 7, p. 76006, 2013.
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[22] Z. Hu, X. Wu, Y. Ouyang, Y. Ouyang, and S. R. Sadda, “Semiautomated segmentation of the choroid in spectraldomain optical coherence tomography volume scans,” Invest Ophthalmol Vis Sci , vol. 54, no. 3, pp. 1722–9, 2013.
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[23] R. Beichel and Y. Wang, “Computer-aided lymph node segmentation in volumetric CT data,” Medical Physics , vol. 39, no. 9, pp. 5419–5428, 2012. (PMCID: PMC3432102).
[24] S. Sun, C. Bauer, and R. Beichel, “Automated 3D segmentation of lungs with lung cancer in CT data using a novel robust active shape model approach,” IEEE Trans. Med. Imag.
, vol. 31, no. 2, p. 449460, 2012. (PMCID: PMC3657761).
[25] C. Bauer, S. Sun, W. Sun, J. Otis, A. Wallace, B. J. Smith, J. J. Sunderland, M. M. Graham, M. Sonka, and J. M.
B. R. R. Beichel, “Automated measurement of uptake in cerebellum, liver, and aortic arch in full-body FDG PET/CT scans,” Medical Physics , vol. 39, no. 6, pp. 3112–3123, 2012. (PMCID: PMC3365916).
[26] S. Sun, M. Sonka, and R. Beichel, “Graph-based IVUS segmentation with efficient computer-aided refinement,” IEEE
Trans. Med. Imag.
, vol. 32, no. 8, pp. 1536–1549, 2013. (PMCID: in process).
[27] S. Sun, M. Sonka, and R. Beichel, “Lung segmentation refinement based on optimal surface finding utilizing a hybrid desktop/virtual reality user interface,” Computerized Medical Imaging and Graphic , vol. 37, no. 1, pp. 15–27, 2013.
(PMCID: in process).
[28] S. Sun, C. Bauer, and R. Beichel, “Robust active shape model based lung segmentation in CT scans,” in Fourth
International Workshop on Pulmonary Image Analysis , pp. 213–223, 2011.
[29] S. Sun, M. Sonka, and R. Beichel, “Graph-based 4d lung segmentation in CT images with expert-guided computeraided refinement,” in IEEE 10th International Symposium on Biomedical Imaging (ISBI) , pp. 1312–1315, April 2013.
[30] C. Bauer, S. Sun, and R. Beichel, “Avoiding mesh folding in 3D optimal surface segmentation,” in 7th International
Symposium on Visual Computing, LNCS 6938 , pp. 214–223, 2011.
[31] Y. Wang and R. Beichel, “Graph-based segmentation of lymph nodes in CT data,” in Advances in Visual Computing,
LNCS 6454 , pp. 312–321, 2010.
[32] C. Olsson, J. Ulen, Y. Boykov, and V. Kolmogorov, “Partial enumeration and curvature regularization,” in International
Conference on Computer Vision (ICCV) , (Sydney, Australia), December 2013.
[33] L. Gorelick, F. R. Schmidt, and Y. Boykov, “Fast trust region for segmentation,” in IEEE conference on Computer
Vision and Pattern Recognition (CVPR) , (Portland, Oregon), pp. 1714–1721, June 2013.
[34] I. B. Ayed, L. Gorelick, and Y. Boykov, “Auxiliary cuts for general classes of higher order functionals,” in IEEE conference on Computer Vision and Pattern Recognition (CVPR) , (Portland, Oregon), pp. 1304–1311, June 2013.
[35] L. Gorelick, F. Schmidt, Y. Boykov, and A. Delong, “Segmentation with non-linear regional constraints via line-search cuts,” in European Conference on Computer Vision (ECCV), LNCS 7572 , vol. 1, (Florence, Italy), pp. 583–597,
October 2012.
[36] M. K. Garvin, M. D. Abr `amoff, K. Lee, M. Niemeijer, M. Sonka, and Y. H. Kwon, “2-d pattern of nerve fiber bundles in glaucoma emerging from spectral-domain optical coherence tomography,” Investigative ophthalmology & visual science , vol. 53, pp. 483–9, Jan 2012. PMCID: PMC22222272.

[37] X. Liu, D. Z. Chen, M. H. Tawhai, X. Wu, E. A. Hoffman, and M. Sonka, “Optimal graph search based segmentation of airway tree double surfaces across bifurcations,” IEEE Trans Med Imaging , vol. 32, pp. 493–510, Mar 2013. PMCID:
PMC23070299.
[38] L. Zhang, K. Lee, M. Niemeijer, R. F. Mullins, M. Sonka, and M. D. Abramoff, “Automated segmentation of the choroid from clinical sd-oct,” Investigative ophthalmology & visual science , Oct 2012. PMCID: PMC23060139.
[39] M. D. Abr `amoff, M. K. Garvin, and M. Sonka, “Retinal imaging and image analysis,” IEEE Rev Biomed Eng , vol. 3, pp. 169–208, Jan 2010. PMCID: PMC22275207.
[40] M. D. Abr `amoff, K. Lee, M. Niemeijer, W. L. M. Alward, E. C. Greenlee, M. K. Garvin, M. Sonka, and Y. H. Kwon,
“Automated segmentation of the cup and rim from spectral domain oct of the optic nerve head,” Investigative ophthalmology & visual science , vol. 50, pp. 5778–84, Dec 2009. PMCID: PMC19608531.
[41] K. Lee, M. Niemeijer, M. K. Garvin, Y. H. Kwon, M. Sonka, and M. D. Abramoff, “Segmentation of the optic disc in 3-d oct scans of the optic nerve head,” IEEE Trans Med Imaging , vol. 29, pp. 159–68, Jan 2010. PMCID: PMC19758857.
[42] R. K. Johnson, S. Premraj, S. S. Patel, N. Walker, A. Wahle, M. Sonka, and T. D. Scholz, “Automated analysis of four-dimensional magnetic resonance images of the human aorta,” Int J Cardiovasc Imaging , vol. 26, pp. 571–8, Jun
2010. PMCID: PMC20146003.
[43] H. W. van Dijk, P. H. B. Kok, M. Garvin, M. Sonka, J. H. Devries, R. P. J. Michels, M. E. J. van Velthoven, R. O.
Schlingemann, F. D. Verbraak, and M. D. Abr `amoff, “Selective loss of inner retinal layer thickness in type 1 diabetic patients with minimal diabetic retinopathy.,” Investigative Ophthalmology & Visual Science , vol. 50, pp. 3404–9, July
2009. PMCID: PMC19151397.
[44] H. W. van Dijk, F. D. Verbraak, P. H. B. Kok, M. K. Garvin, M. Sonka, K. Lee, J. H. Devries, R. P. J. Michels, M. E. J.
van Velthoven, R. O. Schlingemann, and M. D. Abr `amoff, “Decreased retinal ganglion cell layer thickness in patients with type 1 diabetes.,” Investigative Ophthalmology & Visual Science , vol. 51, pp. 3660–5, July 2010. PMCID:
PMC20130282.
[45] H. W. van Dijk, F. D. Verbraak, M. Stehouwer, P. H. B. Kok, M. K. Garvin, M. Sonka, J. H. Devries, R. O. Schlingemann, and M. D. Abr `amoff, “Association of visual function and ganglion cell layer thickness in patients with diabetes mellitus type 1 and no or minimal diabetic retinopathy,” Vision Research , vol. 51, no. 2, pp. 224–228, 2011.
[46] Y. Yin, X. Zhang, R. Williams, X. Wu, D. Anderson, and M. Sonka, “LOGISMOS-Layered optimal graph image segmentation of multiple objects and surfaces: Cartilage segmentation in the knee joint,” IEEE Trans. Med. Imaging , vol. 29, pp. 2023–2037, 2010. PMCID: PMC3131162.
[47] S. Kashyap, Y. Yin, and M. Sonka, “Automated analysis of cartilage morphology,” in Biomedical Imaging (ISBI), 2013
IEEE 10th International Symposium on , pp. 1300–1303, IEEE, 2013.
[48] Y. Yin, Q. Song, and M. Sonka, “Electric field theory motivated graph construction for optimal medical image segmentation,” GbRPR , vol. LNCS 5534, pp. 334–342, 2009.
[49] G. Quellec, K. Lee, M. Dolejsi, M. K. Garvin, M. D. Abr `amoff, and M. Sonka, “Three-dimensional analysis of retinal layer texture: identification of fluid-filled regions in sd-oct of the macula,” IEEE Trans Med Imaging , vol. 29, pp. 1321–
30, Jun 2010. PMCID: PMC20363675.
[50] B. Antony, M. D. Abr `amoff, L. Tang, W. D. Ramdas, J. R. Vingerling, N. M. Jansonius, K. Lee, Y. H. Kwon, M. Sonka, and M. K. Garvin, “Automated 3-d method for the correction of axial artifacts in spectral-domain optical coherence tomography images,” Biomed Opt Express , vol. 2, pp. 2403–16, Aug 2011. PMCID: PMC21833377.
[51] H. Zhang, A. Wahle, R. Johnson, T. Scholz, and M. Sonka, “4-D cardiac MR image analysis: Left and right ventricular morphology and function,” Medical Imaging, IEEE Transactions on , vol. 29, no. 2, pp. 350–364, 2010. PMCID:
PMC2849009.
[52] H. Zhang, A. K. Abiose, D. Gupta, D. N. Campbell, J. B. Martins, M. Sonka, and A. Wahle, “Novel indices for left-ventricular dyssynchrony characterization based on highly automated segmentation from real-time 3-D echocardiography.,” Ultrasound Med Biol , vol. 39, pp. 72–88, Jan 2013. PMCID: PMC23141901.
[53] R. K. Johnson, S. Premraj, S. S. Patel, A. Wahle, A. Stolpen, M. Sonka, and T. D. Scholz, “Quantitative assessment of the entire thoracic aorta from magnetic resonance images,” Cardiol Young , vol. 21, pp. 170–7, Apr 2011. PMCID:
PMC21205418.
[54] X. Xu, M. Niemeijer, Q. Song, M. Sonka, M. K. Garvin, J. M. Reinhardt, and M. D. Abr `amoff, “Vessel boundary delineation on fundus images using graph-based approach,” IEEE Trans Med Imaging , vol. 30, pp. 1184–91, Jun
2011. PMCID: PMC21216707.

[55] X. Chen, M. Niemeijer, L. Zhang, K. Lee, M. D. Abramoff, and M. Sonka, “Three-dimensional segmentation of fluidassociated abnormalities in retinal oct: probability constrained graph-search-graph-cut,” IEEE Trans Med Imaging , vol. 31, pp. 1521–31, Aug 2012. PMCID: PMC22453610.
[56] K. Lee, R. K. Johnson, Y. Yin, A. Wahle, M. E. Olszewski, T. D. Scholz, and M. Sonka, “Three-dimensional thrombus segmentation in abdominal aortic aneurysms using graph search based on a triangular mesh,” Comput Biol Med , vol. 40, pp. 271–8, Mar 2010. PMCID: PMC20074719.
[57] M. K. Garvin, M. D. Abr `amoff, X. Wu, S. R. Russell, T. L. Burns, and M. Sonka, “Automated 3-D intraretinal layer segmentation of macular spectral-domain optical coherence tomography images,” IEEE Trans Med Imaging , vol. 28, pp. 1436–47, Sep 2009. PMCID: PMC19278927.
[58] K. Lee, Y. H. Kwon, M. K. Garvin, M. Niemeijer, M. Sonka, and M. D. Abr `amoff, “Distribution of damage to the entire retinal ganglion cell pathway: quantified using spectral-domain optical coherence tomography analysis in patients with glaucoma,” Arch Ophthalmol , vol. 130, pp. 1118–26, Sep 2012. PMCID: PMC22965586.
[59] F. Zhao, H. Zhang, A. Wahle, M. T. Thomas, A. H. Stolpen, T. D. Scholz, and M. Sonka, “Congenital aortic disease:
4d magnetic resonance segmentation and quantitative analysis,” Medical Image Analysis , vol. 13, pp. 483–93, Jun
2009. PMCID: PMC19303351.
[60] I. Oguz, H. Zhang, A. Rumple, and M. Sonka, “RATS: Rapid automatic tissue segmentation in rodent brain MRI,” J
Neurosci Methods , vol. [Epub ahead of print], p. doi: 10.1016/j.jneumeth.2013.09.021, 2013. PMCID: In process.
[61] K. Lee, M. Sonka, Y. H. Kwon, M. K. Garvin, and M. D. Abramoff, “Adjustment of the retinal angle in SD-OCT of glaucomatous eyes provides better intervisit reproducibility of peripapillary RNFL thickness,” Investigative ophthalmology
& visual science , vol. 54, pp. 4808–4812, 2013. PMCID: PMC3720146.
[62] X. Chen, P. Hou, C. Jin, W. Zhu, X. Luo, F. Shi, M. Sonka, and H. Chen, “Quantitative analysis of retinal layer optical intensities on three-dimensional optical coherence tomography,” Investigative ophthalmology & visual science , vol. 54, pp. 6846–6851, 2013. PMCID: In process, PMID: 24045992.
[63] M. K. Garvin, K. Lee, T. L. Burns, M. D. Abramoff, M. Sonka, and Y. H. Kwon, “Reproducibility of sd-oct-based ganglion cell-layer thickness in glaucoma using two different segmentation algorithms,” Investigative ophthalmology
& visual science , vol. 54, pp. 6998–7004, 2013. PMCID: PMC3809946.
[64] M. D. Abramoff, R. F. Mullins, K. Lee, J. M. Hoffmann, M. Sonka, D. B. Critser, S. F. Stasheff, and E. M. Stone, “Human photoreceptor outer segments shorten during light adaptation,” Investigative ophthalmology & visual science , vol. 54, pp. 3721–3728, 2013. PMCID: PMC3668803.
[65] N. Demirkaya, S. M. van Schuppen, M. D. Abramoff, M. K. Garvin, M. Sonka, R. O. Schlingemann, and F. D. Verbraak,
“Effect of age on individual retinal layer thickness in normal eyes as measured with spectral-domain optical coherence tomography,” Investigative ophthalmology & visual science , vol. 54, pp. 4934–4940, 2013. PMID: 23761080.
[66] T. Kovarnik, A. Kral, H. Skalicka, L. Skalicka, O. Dostal, L. Kralik, P. Martasek, M. Aschermann, J. Horak, A. Linhart,
A. Wahle, and M. Sonka, “Prediction of coronary vessel involvement on the basis of atherosclerosis risk factor analysis,” Bratisl Lek Listy , vol. 114, pp. 413–417, 2013. PMCID: In process, PMID: 23822628.
[67] T. Kovarnik, A. Kral, H. Skalicka, G. S. Mintz, L. Kralik, M. Chval, J. Horak, L. Skalicka, M. Sonka, A. Wahle, R. W.
Downe, J. Uhrova, H. Benakova, L. Cernohousova, P. Martasek, J. Belohlavek, M. Aschermann, and A. Linhart, “The prediction of coronary artery disease based on non-invasive examinations and heme oxygenase 1 polymorphism versus virtual histology,” J Invasive Cardiol , vol. 25, pp. 32–37, 2013. PMCID: In process – PMID: 23293173.
[68] R. Kafieh, H. Rabbani, M. D. Abramoff, and M. Sonka, “Curvature correction of retinal octs using graph-based geometry detection,” Phys Med Biol , vol. 58, pp. 2925–2938, 2013. PMCID: PMC3794717.
[69] E. H. Sohn, J. J. Chen, K. Lee, M. Niemeijer, M. Sonka, and M. D. Abramoff, “Reproducibility of diabetic macular edema estimates from SD-OCT is affected by the choice of image analysis algorithm,” Investigative ophthalmology
& visual science , vol. 54, pp. 4184–4188, 2013. PMCID: PMC3687962.
[70] K. Li, X. Wu, D. Z. Chen, and M. Sonka, “Optimal surface segmentation in volumetric images — A graph-theoretic approach,” IEEE Transactions on Pattern Analysis and Machine Intelligence , vol. 28, no. 1, pp. 119–134, 2006.
[71] A. Wahle, J. J. Lopez, M. E. Olszewski, S. C. Vigmostad, K. B. Chandran, J. D. Rossen, and M. Sonka, “Plaque development, vessel curvature, and wall shear stress in coronary arteries assessed by X-ray angiography and intravascular ultrasound,” Medical Image Analysis — Functional Imaging and Modeling of the Heart , vol. 10, pp. 615–631, Aug.
2006.
[72] X. Wu, D. Z. Chen, K. Li, and M. Sonka, “The layered net surface problems in discrete geometry and medical image segmentation,” International Journal of Computational Geometry and Applications — Selected Papers from the 16th
ISAAC Conference , vol. 17, pp. 261–296, June 2007.

[73] X. Wu and M. B. Merickel, “Simultaneous border segmentation of doughnut-shaped objects in medical images,”
Journal of Graph Algorithms and Applications , vol. 11, no. 1, pp. 215–237, 2007.
[74] M. K. Garvin, M. D. Abr `amoff, R. Kardon, S. R. Russell, X. Wu, and M. Sonka, “Intraretinal layer segmentation of macular optical coherence tomography images using optimal 3-D graph search,” IEEE Transactions on Medical
Imaging , vol. 27, pp. 1495–1505, Oct. 2008.
[75] K. Li, S. Millington, X. Wu, D. Z. Chen, and M. Sonka, “Simultaneous segmentation of multiple closed surfaces using optimal graph searching,” in Information Processing in Medical Imaging (IPMI 2005) (G. E. Christensen and
M. Sonka, eds.), vol. 3565 of Lecture Notes in Computer Science , (Berlin/New York), pp. 406–417, Springer, 2005.
[76] X. Wu, D. Z. Chen, K. Li, and M. Sonka, “The layered net surface problems in discrete geometry and medical image segmentation,” in 16th Annual International Symposium on Algorithms and Computation (ISAAC) (X. Deng and D. Du, eds.), vol. 3827 of Lecture Notes in Computer Science , (Berlin/New York), pp. 17–27, Springer, 2005.
[77] M. K. Haeker, M. D. Abr `amoff, R. Kardon, and M. Sonka, “Segmentation of the surfaces of the retinal layer from OCT images,” in Medical Image Computing and Computer-Assisted Intervention (MICCAI 2006) (R. Larsen, M. Nielsen, and J. Sporring, eds.), vol. 4190 of Lecture Notes in Computer Science , (Berlin/New York), pp. 800–807, Springer,
2006.
[78] M. S. Hansen, F. Zhao, H. Zhang, N. E. Walker, A. Wahle, T. D. Scholz, and M. Sonka, “Detection of connective tissue disorders from 3-D aortic MR images using independent component analysis,” in Computer Vision Approaches to
Medical Image Analysis (CVAMIA06) (R. Beichel and M. Sonka, eds.), vol. 4241 of Lecture Notes in Computer
Science , (Berlin/New York), pp. 13–24, Springer, 2006.
[79] M. S. Hansen, F. Zhao, H. Zhang, B. K. Ersbøll, A. Wahle, T. D. Scholz, and M. Sonka, “Diagnosis of connective tissue disorders based on independent component analysis of aortic shape and motion from 4-D MR images,” in The
1st International Workshop on Computer Vision for Intravascular and Intracardiac Imaging (MICCAI 2006) (G. ¨
I. A. Kakadiaris, G. Slabaugh, and A. Tannenbaum, eds.), (Frederiksberg), pp. 154–161, Samfundslitteratur, 2006.
[80] M. B. Merickel, X. Wu, M. Sonka, and M. D. Abr `amoff, “Optimal segmentation of the optic nerve head from stereo retinal images,” in Medical Imaging 2006: Physiology, Function, and Structure from Medical Images (A. Manduca and
A. A. Amini, eds.), vol. 6143, (Bellingham WA), pp. 61433B.1–61433B.8, SPIE Proceedings, 2006.
[81] M. Sonka, F. Zhao, H. Zhang, A. Wahle, and T. D. Scholz, “Early detection of aortic aneurysm risk from 4-D MR image data,” in Proc. Computers in Cardiology 2006, Valencia , vol. 33, (Piscataway NJ), pp. 69–72, IEEE Press, 2006.
[82] S. Ukil, M. Sonka, and J. M. Reinhardt, “Automatic segmentation of pulmonary fissures in X-ray CT images using anatomic guidance,” in Medical Imaging 2006: Image Processing (J. M. Reinhardt and J. P. W. Pluim, eds.), vol. 6144,
(Bellingham WA), pp. 61440N.1–61440N.11, SPIE Proceedings, 2006.
[83] X. Wu, “Efficient algorithms for the optimal-ratio region detection problems in discrete geometry with applications,” in
17th Annual International Symposium on Algorithms and Computation (ISAAC) (T. Asano, ed.), vol. 4288 of Lecture
Notes in Computer Science , (Berlin/New York), pp. 289–299, Springer, 2006.
[84] F. Zhao, H. Zhang, N. E. Walker, F. Yang, M. E. Olszewski, A. Wahle, T. D. Scholz, and M. Sonka, “Quantitative analysis of two-phase 3D+time aortic MR images,” in Medical Imaging 2006: Image Processing (J. M. Reinhardt and
J. P. W. Pluim, eds.), vol. 6144, (Bellingham WA), pp. 699–708, SPIE Proceedings, 2006.
[85] F. Zhao, H. Zhang, A. Wahle, T. D. Scholz, and M. Sonka, “Automated 4-D segmentation of aortic magnetic resonance images,” in British Machine Vision Conference 2006 (M. J. Chantler, E. Trucco, and R. B. Fisher, eds.), vol. 1, (Worcs), pp. 247–256, BMVA, 2006.
[86] M. K. Haeker, M. Sonka, R. Kardon, V. A. Shah, X. Wu, and M. D. Abr `amoff, “Automated segmentation of intraretinal layers from macular optical coherence tomography images,” in Medical Imaging 2007: Image Processing (J. P. W.
Pluim and J. M. Reinhardt, eds.), vol. 6512, (Bellingham WA), pp. 651214.1–651214.11, SPIE Proceedings, 2007.
[87] M. K. Haeker, X. Wu, M. D. Abr `amoff, R. Kardon, and M. Sonka, “Incorporation of regional information in optimal
3-D graph search with application for intraretinal layer segmentation of optical coherence tomography,” in Information
Processing in Medical Imaging (IPMI 2007) (N. Karssemeijer and B. P. F. Lelieveldt, eds.), vol. 4584 of Lecture Notes in Computer Science , (Berlin/New York), pp. 607–618, Springer, 2007.
[88] M. K. Haeker, M. D. Abr `amoff, X. Wu, R. Kardon, and M. Sonka, “Use of varying constraints in optimal 3-D graph search for segmentation of macular optical coherence tomography images,” in Medical Image Computing and
Computer-Assisted Intervention (MICCAI 2007) (N. Ayache, S. Ourselin, and A. Maeder, eds.), vol. 4791 of Lecture
Notes in Computer Science , (Berlin/New York), pp. 244–251, Springer, 2007.
[89] M. B. Merickel, M. D. Abr `amoff, M. Sonka, and X. Wu, “Segmentation of the optic nerve head combining pixel classification and graph search,” in Medical Imaging 2007: Image Processing (J. P. W. Pluim and J. M. Reinhardt, eds.), vol. 6512, (Bellingham WA), pp. 651215.1–651215.10, SPIE Proceedings, 2007.

[90] R. W. Downe, A. Wahle, T. Kov ´arn´ık, H. Skalick ´a, J. J. Lopez, J. Hor ´ak, and M. Sonka, “Segmentation of intravascular ultrasound images using graph search and a novel cost function,” in The 2nd International Workshop on Computer
Vision for Intravascular and Intracardiac Imaging (MICCAI 2008) (G. ¨ eds.), (Istanbul), pp. 71–79, Sabanci University, 2008.
[91] K. M. Lee, Y. Yin, A. Wahle, M. E. Olszewski, and M. Sonka, “3-D segmentation and quantitative analysis of inner and outer walls of thrombotic abdominal aortic aneurysms,” in Medical Imaging 2008: Physiology, Function, and Structure from Medical Images (X. P. Hu and A. V. Clough, eds.), vol. 6916, (Bellingham WA), pp. 691626.1–691626.9, SPIE
Proceedings, 2008.
[92] X. Liu, D. Z. Chen, X. Wu, and M. Sonka, “Optimal graph-based segmentation of 3D pulmonary airway and vascular trees across bifurcations,” in The First International Workshop on Pulmonary Image Analysis (MICCAI 2008)
(M. Brown, M. de Bruijne, B. van Ginneken, A. Kiraly, J. M. Kuhnigk, C. Lorenz, K. Mori, and J. M. Reinhardt, eds.),
(Morrisville), pp. 103–111, Lulu Enterprises, 2008.
[93] Y. Yin, X. Zhang, and M. Sonka, “Optimal multi-object multi-surface graph search segmentation: Full-joint cartilage delineation in 3D,” in Medical Image Understanding and Analysis 2008 (S. McKenna and J. Hoey, eds.), pp. 104–108,
British Machine Vision Association, 2008.
[94] X. Liu, D. Z. Chen, X. Wu, and M. Sonka, “Optimal graph search based image segmentation for objects with complex topologies,” in Medical Imaging 2009: Image Processing (J. P. W. Pluim and B. M. Dawant, eds.), vol. 7259,
(Bellingham WA), SPIE Proceedings, 2009.
[95] Q. Song, X. Wu, and M. Sonka, “Globally optimal 3D graph search incorporating both edge and regional information:
Application to aortic MR image segmentation,” in Medical Imaging 2009: Image Processing (J. P. W. Pluim and B. M.
Dawant, eds.), vol. 7259, (Bellingham WA), SPIE Proceedings, 2009.
[96] F. Zhao, H. Zhang, A. Wahle, M. T. Thomas, A. H. Stolpen, T. D. Scholz, and M. Sonka, “Computer-aided diagnosis of congenital aortic disease using aortic shape and motion,” American Heart Association, Scientific Sessions, Chicago
IL, Circulation (Supplement) , vol. 114, Oct. 2006. Abstract 3652.
[97] M. Sonka, X. Zhang, and S. Millington, “Three-dimensional segmentation and analysis of articular cartilage,” in
Workshop on Imaging-Based Measures of Osteoarthritis , (Salzburg), Paracelsus University, 2007. Abstract P104.
[98] Y. Yin, X. Zhang, and M. Sonka, “Fully three-dimensional segmentation of articular cartilage performed simultaneously in all bones of the joint,” 2007 World Congress on Osteoarthritis (OARSI), Osteoarthritis and Cartilage
(Supplement) , vol. 15, p. C177, Dec. 2007. Abstract 318.
[99] F. Zhao, A. H. Stolpen, D. R. Thedens, H. Zhang, T. D. Scholz, A. Wahle, and M. Sonka, “Automated segmentation of 4D cine MRI: Application to the aortic root and quantitative comparison of normal subjects and patients with marfan syndrome.,” in Joint Annual Meeting of the International Society for Magnetic Resonance in Medicine and the European Society for Magnetic Resonance in Medicine and Biology 2007, Berlin, Germany , (Berkeley), p. 504,
ISMRM, 2007. Abstract 2593.
[100] F. Zhao, H. Zhang, A. Wahle, M. T. Thomas, A. H. Stolpen, T. D. Scholz, and M. Sonka, “Classification of aortic connective tissue disorder from 4D MR image data based on principal component analysis and support vector machine,” CARS 2007, 21st International Congress and Exhibition, Berlin, Germany, International Journal of Computer
Assisted Radiology and Surgery (Supplement) , vol. 2, pp. S519–S520, June 2007.
[101] Q. Song, X. Wu, Y. Yin, M. Chen, Y. Kim, J. E. Bayouth, J. M. Buatti, R. A. C. Siochi, and M. Sonka, “Simultaneous segmentation of bladder and prostate using globally optimal 3-D graph search method,” 50th Annual Meeting of the
American Society for Therapeutic Radiology and Oncology (ASTRO), International Journal of Radiation Oncology,
Biology, and Physics (Supplement) , vol. 72, p. S148, Sept. 2008. Abstract 1077.
[102] X. Dou, X. Wu, L. Xing, and J. E. Bayouth, “Analysis of breathing pattern for radiotherapy by studying diaphragm trajectory,” 50th Annual Meeting of the American Association of Physicists in Medicine (AAPM), Houston, Medical
Physics (Supplement) , vol. 35, p. 2663, June 2008. Abstract SU-GG-I-94.
[103] A. Delong and Y. Boykov, “A Scalable Graph-Cut Algorithm for N-D Grids,” in Comp. Vision and Pattern Recognition
(CVPR) , 2008.
[104] A. Delong and Y. Boykov, “Globally Optimal Segmentation of Multi-Region Objects,” in International Conference on
Computer Vision (ICCV) , 2009.
[105] X. Dou, X. Wu, S. Bhatia, and J. Buatti, “Tumor segmentation in ct images using globally optimal single surface detection,” Medical Physics , vol. 37, no. 6, pp. 3459–3459, 2010.
[106] B. J. Antony, M. D. Abramoff, M. M. Harper, W. Jeong, E. H. Sohn, Y. H. Kwon, R. H. Kardon, and M. K. Garvin,
“A combined machine-learning and graph-based framework for the segmentation of retinal surfaces in SD-OCT volumes,” Biomed. Opt. Express , vol. 4, p. In Press, 2014.

[107] B. J. Antony, Q. Song, M. D. Abramoff, E. H. Sohn, X. Wu, and M. K. Garvin, “Incorporation of learned shape priors into a graph-theoretic approach with application to the 3-D segmentation of intraretinal surfaces in SD-OCT volumes of mice,” in SPIE Medical Imaging 2014: Biomedical Applications in Molecular, Structural, and Functional Imaging ,
(Bellingham, WA), p. In Press, SPIE, 2014.
[108] A. Rashid, U. Schmidt-Erfurth, B. S. Gerendas, S. M. Waldstein, H. Bogunovic, A. Wahle, C. Simader, K. Lee,
M. Sonka, and M. D. Abramof, “Total retinal thickness using iowa reference algorithm: Measurement reproducibility in 5 SD-OCT scanners,” in ARVO 2013 Annual Meeting Abstracts , p. 5503, Association for Research in Vision and
Ophthalmology, Inc, 2013.