Milan Sonka, PhD

Associate Dean, College of Engineering
Co-director, Iowa Institute for Biomedical Imaging
Professor of Electrical and Computer Engineering (ECE)
Professor of Radiation Oncology
Professor of Ophthalmology and Visual Sciences
Professor of Biomedical Engineering (BME)

Contact Information

Iowa City, IA 52242

Office: 4013 Seamans Center
Iowa City, IA 52242

Primary Office: 3016B SC


Center, Program and Institute Affiliations

Aging Mind and Brain Initiative, Iowa Institute for Biomedical Imaging


Guo, Z., Kwon, Y. H., Lee, K., Wang, K., Wahle, A., Alward WLM,, Fingert, J. H., Bettis, D. I., Johnson, C. A., Garvin, M. K., Sonka, M. & Abràmoff, M. D. (2017). Optical Coherence Tomography Analysis Based Prediction of Humphrey 24-2 Visual Field Thresholds in Patients With Glaucoma. Investigative ophthalmology & visual science, 58(10), 3975-3985. PMID: 28796875.

Klein, B. E., Johnson, C. A., Meuer, S. M., Lee, K., Wahle, A., Lee, K. E., Kulkarni, A., Sonka, M., Abràmoff, M. D. & Klein, R. (2017). Nerve Fiber Layer Thickness and Characteristics Associated with Glaucoma in Community Living Older Adults: Prelude to a Screening Trial?. Ophthalmic epidemiology, 24(2), 104-110. PMID: 28032805.

Miri, M. S., Abràmoff, M. D., Kwon, Y. H., Sonka, M. & Garvin, M. K. (2017). A machine-learning graph-based approach for 3D segmentation of Bruch's membrane opening from glaucomatous SD-OCT volumes. Medical image analysis, 39, 206-217. PMID: 28528295.

Klimscha, S., Waldstein, S. M., Schlegl, T., Bogunovic, H., Sadeghipour, A., Philip, A. M., Podkowinski, D., Pablik, E., Zhang, L., Abramoff, M. D., Sonka, M., Gerendas, B. S. & Schmidt-Erfurth, U. (2017). Spatial Correspondence Between Intraretinal Fluid, Subretinal Fluid, and Pigment Epithelial Detachment in Neovascular Age-Related Macular Degeneration. Investigative ophthalmology & visual science, 58(10), 4039-4048. PMID: 28813577.

Guo, Z., Kashyap, S., Sonka, M. & Oguz, I. (2017). Machine learning in a graph framework for subcortical segmentation. Proceedings of SPIE, 10133. PMID: 28626291.

Kovarnik, T., Chen, Z., Wahle, A., Zhang, L., Skalicka, H., Kral, A., Lopez, J. J., Horak, J., Sonka, M. & Linhart, A. (2017). Pathologic Intimal Thickening Plaque Phenotype: Not as Innocent as Previously Thought. A Serial 3D Intravascular Ultrasound Virtual Histology Study. Revista espanola de cardiologia (English ed.), 70(1), 25-33. PMID: 27615562.


Lee, K., Zhang, H., Wahle, A., Abràmoff, M. D. & Sonka, M. (2017). Multi-layer 3D Simultaneous Retinal OCT Layer Segmentation: Just-Enough Interaction for Routine Clinical Use. In European Congress on Computational Methods in Applied Sciences and Engineering. pp. 862–871. VipImage.

Pazdernik, M., Bedanova, H., Kautzner, J., Melenovsky, V., Karmazin, V., Tomasek, A., Kovarnik, T., Malek, I., Wahle, A., Chen, Z. & others, (2017). Insights to pathophysiology and risk factors of cardiac allograft vasculopathy: A prospective study using highly automated coronary optical coherence tomography segmentation software in 3D. (Vols. 38). (suppl_1) European Heart Journal.

Zhang, L., Kong, H., Liu, S., Wang, T., Chen, S. & Sonka, M. (2017). Graph-based segmentation of abnormal nuclei in cervical cytology. Computerized medical imaging and graphics: the official journal of the Computerized Medical Imaging Society, 56, 38-48. PMID: 28222324.

Xiang, D., Bagci, U., Jin, C., Shi, F., Zhu, W., Yao, J., Sonka, M. & Chen, X. (2017). CorteXpert: A model-based method for automatic renal cortex segmentation. Medical image analysis, 42, 257-273. PMID: 28888170.

Sohn, E. H., van Dijk, H. W., Jiao, C., Kok, P. H., Jeong, W., Demirkaya, N., Garmager, A., Wit, F., Kucukevcilioglu, M., van Velthoven, M. E., DeVries, J. H., Mullins, R. F., Kuehn, M. H., Schlingemann, R. O., Sonka, M., Verbraak, F. D. & Abramoff, M. D. (2016). Retinal neurodegeneration may precede microvascular changes characteristic of diabetic retinopathy in diabetes mellitus. Proceedings of the National Academy of Sciences USA, 113(19), E2655-E64. PMID: 27114552.

Sonka, M., Abràmoff, M. D. (2016). Quantitative analysis of retinal OCT. Medical image analysis, 33, 165-169. PMID: 27503080.

Korvarnik, T., Jerabek, S., Chen, Z., Wahle, A., Zhang, L., Dostalova, G., Skalicka, H., Kral, A., Horak, J., Sonka, M. & Linhart, A. (2016). Non-invasive endothelial function assessment using digital reactive hyperemia correlates with 3D intravascular ultrasound and virtual histology-derived plaque volume and plaque phenotype. Kardiologia Polska. PMID: 27160175.

Kashyap, S., Oguz, I., Zhang, H. & Sonka, M. (2016). Automated Segmentation of Knee MRI Using Hierarchical Classifiers and Just Enough Interaction Based Learning: Data from Osteoarthritis Initiative. Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention, 9901, 344-351. PMID: 28626842.

Philip, A. M., Gerendas, B. S., Zhang, L., Faatz, H., Podkowinski, D., Bogunovic, H., Abramoff, M. D., Hagmann, M., Leitner, R., Simader, C., Sonka, M., Waldstein, S. M. & Schmidt-Erfurth, U. (2016). Choroidal thickness maps from spectral domain and swept source optical coherence tomography: algorithmic versus ground truth annotation. British journal of ophthalmology, 100(10), 1372-1376. PMID: 26769670.

Oguz, I., Kashyap, S., Wang, H., Yushkevich, P. & Sonka, M. (2016). Globally Optimal Label Fusion with Shape Priors. Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention, 9901, 538-546. PMID: 28626843.

Hirai, T., Chen, Z., Zhang, L., Baaj, S., Kovarnik, T., Porcaro, K., Kaminski, J., Hawn, S., Agrawal, A., Makki, N., Downe, R., Wahle, A., Sonka, M. & Lopez, J. J. (2016). Evaluation of Variable Thin-Cap Fibroatheroma Definitions and Association of Virtual Histology-Intravascular Ultrasound Findings With Cavity Rupture Size. American journal of cardiology, 118(2), 162-169. PMID: 27289292.

Lee, K., Buitendijk, G. H., Bogunovic, H., Springelkamp, H., Hofman, A., Wahle, A., Sonka, M., Vingerling, J. R., Klaver, C. C. & Abramoff, M. D. (2016). Automated Segmentability Index for Layer Segmentation of Macular SD-OCT Images. Translational Vision Science & Technology, 5(2), 14. PMID: 27066311.

Choi, C. S., Zhang, L., Abramoff, M. D., Sonka, M., Shifera, A. S. & Kay, C. N. (2016). Evaluating Efficacy of Aflibercept in Refractory Exudative Age-Related Macular Degeneration With OCT Segmentation Volumetric Analysis. Ophthalmic Surgery Lasers Imaging Retina, 47(3), 245-51. PMID: 26985798.

Beichel, R. R., Van Tol, M., Ulrich, E. J., Bauer, C., Chang, T., Plichta, K. A., Smith, B. J., Sunderland, J. J., Graham, M. M., Sonka, M. & Buatti, J. M. (2016). Semiautomated segmentation of head and neck cancers in 18F-FDG PET scans: A just-enough-interaction approach. Medical physics, 43(6), 2948-2964. PMID: 27277044.

Oguz, I., Abramoff, M. D., Zhang, L., Lee, K., Zhang, E. Z. & Sonka, M. (2016). 4D Graph-Based Segmentation for Reproducible and Sensitive Choroid Quantification From Longitudinal OCT Scans. Investigative ophthalmology & visual science, 57(9), OCT621-OCT630. PMID: 27936264.

Kafieh, R., Rabbani, H., Hajizadeh, F., Abramoff, M. D. & Sonka, M. (2015). Thickness mapping of eleven retinal layers segmented using the diffusion maps method in normal eyes. Journal of ophthalmology, 2015, 259123. PMID: 25960888.

Oguz, I., Styner, M., Sanchez, M., Shi, Y. & Sonka, M. (2015). LOGISMOS-B for Primates: Primate Cortical Surface Reconstruction and Thickness Measurement. Proceedings of SPIE, 9413. PMID: 26028802.

Chen, H., Chen, X., Qiu, Z., Xiang, D., Chen, W., Shi, F., Zheng, J., Zhu, W. & Sonka, M. (2015). Quantitative analysis of retinal layers' optical intensities on 3D optical coherence tomography for central retinal artery occlusion. Scientific reports, 5, 9269. PMID: 25784298.

Almeida, D. R., Zhang, L., Chin, E. K., Mullins, R. F., Kucukevcilioglu, M., Critser, D. B., Sonka, M., Stone, E. M., Folk, J. C., Abràmoff, M. D. & Russell, S. R. (2015). Comparison of retinal and choriocapillaris thicknesses following sitting to supine transition in healthy individuals and patients with age-related macular degeneration. JAMA ophthalmology, 133(3), 297-303. PMID: 25521616.

Zhang, L., Buitendijk, G. H., Lee, K., Sonka, M., Springelkamp, H., Hofman, A., Vingerling, J. R., Mullins, R. F., Klaver, C. C. & Abràmoff, M. D. (2015). Validity of Automated Choroidal Segmentation in SS-OCT and SD-OCT. Investigative ophthalmology & visual science, 56(5), 3202-3211. PMID: 26024104.

Sonka, M., Hlavac, V. & Boyle, R. (2014). Image Processing, Analysis, and Machine Vision - 4th Ed. (Vols. 890). New York: Cengage Learning.

Bogunovic, H., Kwon, Y. H., Rashid, A., Lee, K., Critser, D. B., Garvin, M. K., Sonka, M. & Abràmoff, M. D. (2014). Relationships of retinal structure and humphrey 24-2 visual field thresholds in patients with glaucoma. Investigative ophthalmology & visual science, 56(1), 259-271. PMID: 25491294.

Zhang, L., Sonka, M., Folk, J. C., Russell, S. R. & Abràmoff, M. D. (2014). Quantifying disrupted outer retinal-subretinal layer in SD-OCT images in choroidal neovascularization. Investigative ophthalmology & visual science, 55(4), 2329-35. PMID: 24569576.

Oguz, I., Zhang, H., Rumple, A. & Sonka, M. (2014). RATS: Rapid Automatic Tissue Segmentation in rodent brain MRI. Journal of neuroscience methods, 221, 175-182. PMID: 24140478.

Gerendas, B. S., Waldstein, S. M., Simader, C., Deak, G., Hajnajeeb, B., Zhang, L., Bogunovic, H., Abramoff, M. D., Kundi, M., Sonka, M. & Schmidt-Erfurth, U. (2014). Three-dimensional automated choroidal volume assessment on standard spectral-domain optical coherence tomography and correlation with the level of diabetic macular edema. American journal of ophthalmology, 158(5), 1039-1048. PMID: 25127697.

Rabbani, H., Sonka, M. & Abramoff, M. D. (2013). Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain. International journal of biomedical imaging, 2013, 417491. PMID: 24222760.

Zhang, H., Abiose, A. K., Gupta, D., Campbell, D. N., Martins, J. B., Sonka, M. & Wahle, A. (2013). Novel indices for left-ventricular dyssynchrony characterization based on highly automated segmentation from real-time 3-d echocardiography. (Vols. 39). (1), pp. 72-88. Ultrasound Med Biol. PMID: 23141901.

Zhang, L., Lee, K., Niemeijer, M., Mullins, R. F., Sonka, M. & Abramoff, M. D. (2012). Automated Segmentation of the Choroid from Clinical SD-OCT. Invest Ophthalmol Vis Sci, 53(12), 7510-9. PMID: 23060139.

Fedorov, A., Beichel, R., Kalpathy-Cramer, J., Finet, J., Fillion-Robin, J., Pujol, S., Bauer, C., Jennings, D., Fennessy, F., Sonka, M., Buatti, J., Aylward, S., Miller, J., Pieper, S. & Kikinis, R. (2012). 3D Slicer As An Image Computing Platform For The Quantitative Imaging Network. Magnetic Resonance Imaging, 30(9), 1323-1341. PMID: 22770690.

Xu, L., Stojkovic, B., Zhu, Y., Song, Q., Wu, X., Sonka, M. & Xu, J. (2011). Efficient algorithms for segmenting globally optimal and smooth multi-surfaces. Information processing in medical imaging, 22, 208-220. PMID: 21761658.

Antony, B., Abramoff, M. D., Tang, L., Ramdas, W. D., Vingerling, J. R., Jansonius, N. M., Lee, K., Kwon, Y. H., Sonka, M. & Garvin, M. K. (2011). Automated 3-D method for the correction of axial artifacts in spectral-domain optical coherence tomography images. Biomed Opt Express, 2(8), 2403-16. PMID: 21833377.

Abramoff, M., Garvin, M. & Sonka, M. (2010). Retinal Imaging and Image Analysis. IEEE Reviews in Biomedical Engineeringÿ, 3, 169-208.

Sonka, M., Hlavac, V. & Boyle, R. (2007). Image Processing, Analysis, and Machine Vision - 3rd Ed. pp. 850 pages. Thomson Engineering, Toronto, Canada.

Li, K., Wu, X., Chen, D. Z. & Sonka, M. (2006). Optimal Surface Segmentation in Volumetric Images-A Graph-Theoretic Approach. IEEE Trans Pattern Anal Mach Intell, 28(1), 119-134. PMID: 16402624.

Christensen, G. E., Sonka, M. (2005). Information Processing in Medical Imaging, Proceedings (series: Lecture Notes in Computer Science Vol. 3565). Springer, Berlin.

Sonka, M., Fitzpatrick, J. M. (2000). Handbook of Medical Imaging Volume 2 - Medical Image Processing and Analysis. pp. 1250 pages. SPIE.