Image courtesy Bryan Jones 2014

I am a Research Scientist with the Scientific Computing and Imaging Institute at the University of Utah and the Director of the Biomedical Image and Data Analysis Core (BIDAC), a University of Utah Core research facility.  I have a background in biology, medical image processing, and software architecture. I also direct a team of software engineers and researchers at the Comprehensive Arryhthmia Research and Management (CARMA) Center in the development of novel MRI-based image analysis techniques and clinical software tools for the management of atrial fibrillation (AF). My research in this area ranges from techniques for measuring the extent and patterning of scar and fibrotic tissue from MRI to the segmentation of cardiac anatomy and multimodal MRI image registration.


As a researcher and engineer, I have almost 15 years of experience designing and implementing medical image registration, segmentation, and visualization algorithms. I have been especially focused on the difficult R&D that often lies in the gap between original innovation and its application to real-world problems. For example, I am one of the original architects of the open-source Insight Toolkit (ITK), which has been helping researchers and commercial engineers in biomedical imaging bridge that gap for almost ten years.  As Director of BIDAC, I coordinate interdisciplinary research collaborations between computer scientists and health sciences researchers. I have also collaborated with the Technology  and Venture Commercialization Office at the University of Utah, where I have engineered prototype software systems for several University spin-off companies and business partners, including work in industrial assembly-line image processing and computational molecular phenotyping.  In addition to my work at the University of Utah, I have also done independent contracting work for various biomedical device start-up companies in the area.


Research Computer Scientist


Oguz, Ipek, Josh Cates, Manasi Datar, Beatriz Paniagua, Thomas Fletcher, Clement Vachet, Martin Styner, and Ross Whitaker (2015). “Entropy-Based Particle Correspondence for Shape Populations”. In: International Journal of Computer Assisted Radiology and Surgery.


Gao, Yi, Liangjia Zhu, Joshua Cates, Rob S MacLeod, Sylvain Bouix, and Allen Tannenbaum (2015). “A Kalman Filtering

Perspective for Multiatlas Segmentation”. In: SIAM Journal on Imaging Sciences 8.2, pp. 1007–1029.


Akoum, Nazem, David Wilber, Gerhard Hindricks, Pierre Jais, Josh Cates, Francis Marchlinkski, Eugene Kholmovski, et al.

(2015a). “MRI Assessment of Ablation-Induced Scarring in Atrial Fibrillation: Analysis from the DECAAF Study”. In: Journal of cardiovascular electrophysiology 26.5, pp. 473–480.


Akoum, Nazem, Alan Morris, Daniel Perry, Josh Cates, Nathan Burgon, Eugene Kholmovski, Rob MacLeod, and Nassir Marrouche (2015). “Substrate Modification Is a Better Predictor of Catheter Ablation Success in Atrial Fibrillation Than Pulmonary Vein Isolation: An LGE-MRI Study”. In: Clinical Medicine Insights. Cardiology 9, p. 25.


Cates, Joshua, Erik Bieging, Alan Morris, Gregory Gardner, Nazem Akoum, Eugene Kholmovski, Nassir Marrouche, Christopher McGann, and Rob S MacLeod (2014). “Computational Shape Models Characterize Shape Change of the Left Atrium in Atrial Fibrillation”. In: Clinical Medicine Insights. Cardiology 8.Suppl 1, p. 99.


Zenger, Brian, Joshua Cates, Alan Morris, Eugene Kholmovski, Alexander Au, Ravi Ranjan, Nazem Akoum, Chris McGann, Brent Wilson, Nassir Marrouche, et al. (2014). “A practical algorithm for improving localization and quantification of left ventricular scar”. In: Computing in Cardiology Conference (CinC), 2014. IEEE, pp. 105–108.


Christopher, McGann, Akoum Nazem, Patel Amit, Kholmovski Eugene, Revelo Patricia, Damal Kavitha, Wilson Brent, Cates Josh, Harrison Alexis, and Ranjan Ravi (2014). “Burgon Nathan S, Greene Tom, Kim Dan, Dibella Edward VR, Parker Dennis, Macleod Rob S, Marrouche Nassir F”. In: Atrial fibrillation ablation outcome is predicted by left atrial remodeling on MRI. Circ Arrhythm Electrophysiol 7.1, pp. 23–30.


Karim, Rashed, R James Housden, Mayuragoban Balasubramaniam, Zhong Chen, Daniel Perry, Ayesha Uddin, Yosra Al Beyatti, Ebrahim Palkhi, Prince Acheampong, Samantha Obom, et al. (2013). “Evaluation of current algorithms for seg-mentation of scar tissue from late Gadolinium enhancement cardiovascular magnetic resonance of the left atrium: an open-access grand challenge”. In: J Cardiovasc Magn Reson 15, p. 105.


McGann, Christopher, Nazem Akoum, Amit Patel, Eugene Kholmovski, Patricia Revelo, Kavitha Damal, Brent Wilson, Josh

Cates, Alexis Harrison, Ravi Ranjan, et al. (2013). “Atrial fibrillation ablation outcome is predicted by left atrial remodeling on MRI”. In: Circulation: Arrhythmia and Electrophysiology, CIRCEP–113.


Gardner, Gregory, Art Morris, Kenichi Higuchi, Rob MacLeod, and Joshua Cates (2013). “A point-correspondence approach to describing the distribution of image features on anatomical surfaces, with application to atrial fibrillation”. In: Biomedical Imaging (ISBI), 2013 IEEE 10th International Symposium on. IEEE, pp. 226–229.


Datar, Manasi, Ilwoo Lyu, SunHyung Kim, Joshua Cates, Martin A Styner, and Ross Whitaker (2013). “Geodesic distances

to landmarks for dense correspondence on ensembles of complex shapes”. In: Medical Image Computing and Computer-Assisted Intervention–MICCAI 2013. Springer, pp. 19–26.


Paniagua, Beatriz, Lucile Bompard, Josh Cates, Ross Whitaker, Manasi Datar, Clement Vachet, and Martin Styner (2012). “Combined SPHARM-PDM and entropy-based particle systems shape analysis framework”. In: SPIE Medical Imaging. International Society for Optics and Photonics, pp. 83170L–83170L.


Zhu, Liangjia, Yi Gao, Anthony Yezzi, Rob MacLeod, Joshua Cates, and Allen Tannenbaum (2012). “Automatic segmentation of the left atrium from MRI images using salient feature and contour evolution”. In: Engineering in Medicine and Biology Society (EMBC), 2012 Annual International Conference of the IEEE. IEEE, pp. 3211–3214.


Perry, D., A. Morris, N. Burgon, C. McGann, R. MacLeod, and J. Cates (2012). “Automatic classification of scar tissue in late gadolinium enhancement cardiac MRI for the assessment of left-atrial wall injury after radiofrequency ablation”. In: Proceedings of SPIE. Vol. 8315, p. 83151D.


Cates, Joshua, Yongsheng Pan, Vianney Battle, and Ross Whitaker (2011). “Cone-beam CT data-driven pose correction for analytic reconstruction methods”. In: SPIE Medical Imaging. International Society for Optics and Photonics, pp. 796139–796139.


McGann, C., E. Kholmovski, J. Blauer, S. Vijayakumar, T. Haslam, J. Cates, E. DiBella, N. Burgon, B. Wilson, A. Alexander, et al. (2011). “Dark regions of no-reflow on late gadolinium enhancement magnetic resonance imaging result in scar formation after atrial fibrillation ablation”. In: Journal of the American College of Cardiology 58.2. PMID 21718914, pp. 177–185.


Vachet, Clement, Heather Cody Hazlett, Marc Niethammer, Ipek Oguz, Joshua Cates, Ross Whitaker, Joseph Piven, and Martin Styner (2011). “Group-wise automatic mesh-based analysis of cortical thickness”. In: SPIE Medical Imaging. International Society for Optics and Photonics, pp. 796227–796227.


Akoum, Nazem, Nathan Burgon, Paul A Anderson, Josh Cates, Eugene Kholmovski, Chris J McGann, Rob MacLeod, Nassir F Marrouche, et al. (2010). “Atrial Fibrosis Assessed Using Delayed-Enhancement MRI Predicts Sinus Node Dysfunction Requiring Pacemaker Implant”. In: Circulation 122.21 Supplement, A16497.


Blauer, JJE, J. Cates, CJ McGann, EG Kholmovski, A. Alexander, MW Prastawa, S. Joshi, NF Marrouche, and RS MacLeod

(2010). “MRI based injury characterization immediately following ablation of atrial fibrillation”. In: Computers in Cardi-ology, 2010. IEEE, pp. 165–168.


Oguz, I, M Neithammer, J Cates, R Whitaker, P T Fletcher, C Vachet, and M Styner (2009). “Cortical Correspondence with Probabilistic Fiber Connectivity”. In: Information Processing in Medical Imaging (IPMI 2009), LNCS 5636. PMID 19694301, pp. 651–663.


Datar, Manasi, Joshua E. Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, and Ross T. Whitaker (Oct. 8, 2009). “Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging.” In: MICCAI (1). Ed. by Guang-Zhong Yang, David J. Hawkes, Daniel Rueckert, J. Alison Noble, and Chris J. Taylor 0002. Vol. 5762. Lecture Notes in Computer Science. Springer, pp. 167–174.


Oguz, I, J Cates, P T Fletcher, Z Warnock, R Whitaker, D Cool, S Aylward, and M Styner (2008). “Cortical Correspondence

Using Entropy-Based Particle Systems and Local Features”. In: Proc. 5th IEEE International Symposium on Biomedical Imaging (ISBI ’08), pp. 1637–1640.


Cates, Joshua, P. Thomas Fletcher, Martin Styner, Heather Cody Hazlett, and Ross Whitaker (2008b). “Particle-Based Shape Analysis of Multi-object Complexes”. In: MICCAI ’08: Proceedings of the 11th international conference on Medical Image Computing and Computer-Assisted Intervention - Part I. PMID 18979781. New York, NY, USA: Springer-Verlag, pp. 477–485. ISBN: 978-3-540-85987-1.


Cates, Joshua, P Thomas Fletcher, Zachary Warnock, and Ross Whitaker (2008a). “A shape analysis framework for small

animal phenotyping with application to mice with a targeted disruption of hoxd11”. In: Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on. IEEE, pp. 512–515.


Cates, Joshua, Thomas Fletcher, and Ross Whitaker (2008). “A hypothesis testing framework for high-dimensional shape

models”. In: 2nd MICCAI Workshop on Mathematical Foundations of Computational Anatomy, pp. 170–181.


Cates, J, P T Fletcher, M Styner, M Shenton, and R Whitaker (2007). “Shape Modeling and Analysis with Entropy-Based

Particle Systems”. In: Information Processing in Medical Imaging (IPMI 2007), LNCS 4584. PMID 1763371, pp. 333–345.


Cates, Joshua, Miriah Meyer, Thomas Fletcher, and Ross Whitaker (2006). “Entropy-based particle systems for shape correspondence”. In: 1st MICCAI Workshop on Mathematical Foundations of Computational Anatomy: Geometrical, Statistical and Registration Methods for Modeling Biological Shape Variability, pp. 90–99.


Cates, J., D. Weinstein, and M. Davis (2006). “The Center for Integrative Biomedical Computing: Advancing biomedical

science with open source”. In: Biomedical Imaging: Nano to Macro, 2006. 3rd IEEE International Symposium on. IEEE, pp. 694–697.


Cates, J.E., R.T. Whitaker, and G.M. Jones (2005). “Case study: an evaluation of user-assisted hierarchical watershed segmentation”. In: Medical Image Analysis 9.6. PMID 15919233, pp. 566–578.


Cates, J.E., A.E. Lefohn, and R.T. Whitaker (2004). “GIST: an interactive, GPU-based level set segmentation tool for 3D

medical images”. In: Medical Image Analysis 8.3. PMID 15450217, pp. 217–231.


Lefohn, A., J. Cates, and R. Whitaker (2003). “Interactive, GPU-based level sets for 3D segmentation”. In: Medical Image

Computing and Computer-Assisted Intervention-MICCAI 2003. PMID 15450217, pp. 564–572.


Ibanez, L., W. Schroeder, L. Ng, and J. Cates (2003). The ITK Software Guide. ISBN 1930934106. Insight Consortium.

Contact Information

Dr. Joshua Cates

Scientific Computing and Imaging Institute

3750 Warnock Engineering Building

72 S Central Campus Drive

University of Utah

Salt Lake City, UT 84112


Office  Location: Warnock Engineering Building (WEB) 2618

Office Number: (801) 581-3996

Fax Number: (801) 585-6513

Email: cates at sci. utah. edu