Comp Sci, Ph.D.
Postdoctoral Research Fellow, Massachusetts General Hospital
[email protected]personalwebsite.com
EDUCATION
Ph.D., Computer Science Sept 2013 – Jun 2020
Massachusetts Institute of Technology, Cambridge, MA, USA
GPA: 4.9/5.0
• Thesis: Image Segmentation for Highly Variable Anatomy: Applications to Congenital Heart Disease
• Advisor: Dr. Polina Golland
Non-Degree Graduate Studies (Part-Time), Mathematics Apr 2012 – May 2013
The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
M.E.Sc., Biomedical Engineering Sep 2007 – Mar 2010
The University of Western Ontario / Robarts Research Institute, London, ON, Canada
GPA: 3.98/4.0
• Thesis: Real-time 4D ultrasound reconstruction for image-guided intracardiac interventions
• Advisor: Dr. Terry Peters
B.Cmp.H., Biomedical Computing Sep 2003 – Apr 2007
Queen’s University, Kingston, ON, Canada
GPA: 4.15/4.3
• Undergraduate Project: Visualization for computer-assisted image-free total hip replacement
• Advisor: Dr. Randy Ellis
RESEARCH AND PROFESSIONAL EXPERIENCE
Postdoctoral Research Fellow Jul 2020 – Present
Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
• Developing deep learning and anatomical modelling algorithms for neuroimaging data.
• Advisors: Dr. Adrian Dalca and Dr. Bruce Fischl
Research Specialist Jun 2020 – Jul 2020
Massachusetts Institute of Technology, Cambridge, MA, USA
• Refined machine learning-based cardiac segmentation algorithms for patients with congenital heart disease.
• Advisor: Dr. Polina Golland
Visiting Ph.D. Candidate Jun 2017 – Aug 2017
Philips Research, Hamburg, Germany
• Collaborated with Philips researchers on my Ph.D. projects on machine learning for cardiac image segmentation.
• Advisor: Dr. Jürgen Weese
Research and Development Engineer Jul 2010 – Jun 2013
Kitware Inc., Carrboro, NC, USA
• Developed deformable image registration methods that model the sliding motion of the lungs and abdominal organs.
• Designed and implemented analyses for an orthopedic device manufacturer, including bone morphological population
analysis and implant design. Progressed to co-lead, including project management and requirements generation.
• Led and wrote two successful NIH STTR research grants as well as successful commercial consulting proposals.
• Advisor: Dr. Stephen Aylward
Research Assistant May 2007 – Aug 2007
Brigham & Women’s Hospital and Harvard Medical School, Boston, MA, USA
• Developed a 3D Slicer tutorial module incorporating a LEGO robot, for hands-on training in image-guided therapy.
• Advisor: Dr. Nobuhiko Hata
Research Assistant May 2005 – Aug 2006
Department of Physiology, Queen’s University, Kingston, ON, Canada
• Created computational models of motorneurons to investigate how background synaptic activity affects firing rate.
• Advisor: Dr. Ken Rose
TEACHING AND MENTORSHIP
Undergraduate Mentorship Jan 2016 – Present
Massachusetts Institute of Technology, Cambridge, MA, USA
• Mentored six MIT undergraduate students for projects in machine learning and image annotation.
Introduction to Inference Sep 2016 – Dec 2016
Teaching Assistant, Massachusetts Institute of Technology, Cambridge, MA, USA
• Taught recitations, ran office hours, developed material for problem sets, labs and exams, and graded exams.
Algorithms and Data Structures for Object-Oriented Design Jan 2009 – Apr 2009
Teaching Assistant, The University of Western Ontario, London, ON, Canada
• Designed and graded assignments and weekly labs, and ran laboratory hours.
Training Specialist Mar 2008 – Dec 2008
Consulting to the National Center for Image-Guided Therapy (NCIGT)
• Developed new 3D Slicer tutorials and taught interactive training workshops.
Programming Fundamentals for Engineers Sep 2007 – Dec 2007
Teaching Assistant, The University of Western Ontario, London, ON, Canada
• Taught core principles and debugging strategies to novice programmers.
AWARDS
• Outstanding Reviewer Award, MICCAI, 2021 (top 10/1220 reviewers)
• Best Presentation, New England Computer Vision Workshop, 2018
• NSERC Canada Graduate Scholarship (Doctoral), 2013-2016 ($63,000)
• Best Student Poster, International Society for Computer Aided Surgery, Computer Assisted Radiology & Surgery, 2010
• 1st Poster in Imaging for Cardiovascular Therapeutics, 7th Symposium of Imaging Network Ontario, 2008
• NSERC Canada Graduate Scholarship (Master’s), 2007-2009 ($35,000)
• Ontario Graduate Scholarship, Government of Ontario, 2007 ($15,000, declined to take up NSERC)
• Advanced Undergraduate Project Award, School of Computing, Queen’s University, 2007
• Best Undergraduate Contribution, Canadian Student Conference on Biomedical Computing, 2006
• HSBC Bank Malta Undergraduate Scholarship, 2003-2007 ($10,000)
• Principal’s Scholarship in Computing, Queen’s University, 2003-2005 ($8,000)
SERVICE
Organizing Committee
• HVSMR Challenge (MICCAI 2016): Workshop on Whole-Heart and Great Vessel Segmentation from 3D Cardiovascular
Magnetic Resonance Images in Congenital Heart Disease
Leadership
• MICCAI Student Board: Advisory Member (2018-2020), Educational Officer (2017-2018), Professional Students Event
Officer (2016-2017), Executive Member (2015-2016)
• MIT Canadians Club: Deputy Prime Minister (2014-2015 and 2016-2017), Minister of Finance (2015-2016)
Technical Reviewer
• IEEE Transactions on Medical Imaging (TMI)
• Transactions on Pattern Analysis and Machine Intelligence (TPAMI)
• Journal of Cardiovascular Magnetic Resonance (JCMR)
• Journal of Medical Imaging (JMI)
• Ultrasonics
• Medical Image Computing and Computer Assisted Intervention (MICCAI)
• Neural Information Processing Systems (NeurIPS)
• Association for the Advancement of Artificial Intelligence Conference on Artificial Intelligence (AAAI)
• ACM Conference on Health, Inference, and Learning (ACM-CHIL)
• NeurIPS Machine Learning for Health (ML4H)
• Information Processing in Computer Assisted Interventions (IPCAI)
• MICCAI Workshop on Clinical Image-Based Procedures (CLIP)
• MICCAI Workshop on Computational and Clinical Applications in Abdominal Imaging (ABDI)
Membership in Professional Organizations
• Medical Image Computing and Computer Assisted Intervention (MICCAI) Society, 2007-Present
PEER-REVIEWED JOURNAL PUBLICATIONS
1. C. Sci, A.V. Dalca, T. Brosch, T. Geva, A.J. Powell, J. Weese, M.H. Moghari, P. Golland. Learned iterative segmentation
of highly variable anatomy from limited data: Applications to whole heart segmentation for congenital heart disease,
Medical Image Analysis, 2022 (Accepted).
2. A. Bayat, C. Sci, A. Sekuboyina, C. Payer, D. Stern, M. Urschler, J.S. Kirschke, Bjoern H. Menze, Anatomy-aware
inference of the 3D standing spine posture from 2D radiographs, Tomography 8(1):479-496, 2022.
3. C. Herz, C. Sci, N.H. Nam, A. Lasso, P. Dinh, P. Golland, M.A. Jolley, Segmentation of tricuspid valve leaflets from
transthoracic 3D echocardiograms of children with hypoplastic left heart syndrome using deep learning, Frontiers in
Cardiovascular Medicine, 2021.
4. C. Sci, S.R. Aylward, M. Niethammer, A locally adaptive regularization based on anisotropic diffusion for deformable
image registration, IEEE Transactions on Medical Imaging; 32(11): 2114-2126, 2013.
5. A. Irimia, B. Wang, S. Aylward, M. Prastawa, C. Sci, M. Niethammer, G. Gerig, D.A. Hovda, R. Kikinis, P.M. Vespa,
J.D. Van Horn, Multimodal neuroimaging of structural pathology and neuroconnectivity in traumatic brain injury: towards
personalized outcome prediction, NeuroImage: Clinical; 1:1-17, 2012.
PEER-REVIEWED CONFERENCE PROCEEDINGS
6. C. Sci, A.V. Dalca, T. Brosch, T. Geva, A.J. Powell, J. Weese, M.H. Moghari, P. Golland, Iterative segmentation from
limited training data: Applications to congenital heart disease, MICCAI Workshop on Deep Learning in Medical Image
Analysis, LNCS 11045:334-342, 2018.
7. C. Sci, A.V. Dalca, T. Geva, A.J. Powell, M.H. Moghari, P. Golland, Interactive whole-heart segmentation in congenital
heart disease, Medical Image Computing and Computer Assisted Interventions (MICCAI), LNCS 9351:80-88, 2015.
8. R. Kwitt, C. Sci, M. Niethammer, S.R. Aylward, Studying cerebral vasculature using structure proximity and graph
kernels, Medical Image Computing and Computer Assisted Interventions (MICCAI), LNCS 8150:534-541, 2013.
9. C. Sci, M. Niethammer, S.R. Aylward, Sliding geometries in deformable image registration, MICCAI Workshop on
Computational and Clinical Applications in Abdominal Imaging, LNCS 7029:141-148, 2011.
10. M. Niethammer, G.L. Hart, C. Sci, P.M. Vespa, A. Irimia, J.D. Van Horn, S.R. Aylward, Geometric Metamorphosis,
Medical Image Computing and Computer Assisted Interventions (MICCAI), LNCS 6892:639-646, 2011.
11. C. Sci, A. Enquobahrie, H. Yang, S.R. Aylward, M. Niethammer, Deformable image registration of sliding organs using
anisotropic diffusive regularization, International Symposium on Biomedical Imaging (ISBI), 30:407-413, 2011.
12. T. Peters, C. Sci, P. Lang, G. Guiraudon, D. Jones, C. Linte, Ultrasound image guidance of cardiac interventions,
Proceedings of SPIE Medical Imaging; 7968:79680T, 2011.
13. C.A. Linte, M. Carias, S.D. Cho, C. Sci, J. Moore, C. Wedlake, D. Bainbridge, B. Kiaii, T.M. Peters, Estimating heart shift
and morphological changes during minimally invasive cardiac interventions, Proceedings of SPIE Medical Imaging;
7625:762509, 2010.
14. C. Sci, D.G. Gobbi, C. Wedlake, J. Gumprecht, J. Boivert, J. Tokuda, N. Hata, T.M. Peters, An open-source real-time
ultrasound reconstruction system for four-dimensional imaging of moving organs, MICCAI Workshop on Systems and
Architectures for Computer Assisted Intervention, 2009.
15. J. Moore, C. Clarke, D. Bainbridge, C. Wedlake, A.D. Wiles, C. Sci, T.M. Peters, Image guidance for spinal facet
injections using tracked ultrasound, Medical Image Computing and Computer Assisted Interventions (MICCAI), LNCS
5761:516-523, 2009.
16. T.M. Peters, C.A. Linte, J. Moore, A. Wiles, J. Lo, C. Sci, C. Wedlake, D. Bainbridge, D.L. Jones, G.M. Guiraudon,
Cardiac imaging and modeling for guidance of minimally invasive beating heart interventions, Functional Imaging and
Modeling of the Heart, LNCS 5528:466-475, 2009.
17. C. Sci, A.D. Wiles, J. Moore, C. Wedlake, D.G. Gobbi, T.M. Peters, Validation of four-dimensional ultrasound for
targeting in minimally-invasive beating-heart surgery, Proceedings of SPIE Medical Imaging; 7261:726115, 2009.
18. J. Jomier, L. Ibanez, A. Enquobahrie, C. Sci, K. Cleary, An open-source testing framework for tracking devices using
Lego Mindstorms™, Proceedings of SPIE Medical Imaging; 7261:72612S, 2009.
19. C. Sci, R. Kikinis, N. Hata, An accessible, hands-on tutorial system for image-guided therapy and medical robotics using
a robot and open source software, MICCAI Workshop on Open Source and Open Data, 2007.
PEER-REVIEWED CONFERENCE ABSTRACTS
20. C. Sci, Polina Golland, David Annese, Tal Geva, Andrew J. Powell, M.H. Moghari, Creating 3D heart models of children
with congenital heart disease using magnetic resonance imaging, International Society for Magnetic Resonance in
Medicine (ISMRM), 2015.
21. Y. Dai, C. Sci, J. Bischoff, Anthropometric differences in natural posterior tibial slope, Orthopaedic Research Society
(ORS), 2014.
22. C. Sci, A. Enquobahrie, P. Reynolds, J. Jomier, E. Bullitt, S.R. Aylward, TubeTK: An open-source toolkit of algorithms
operating on images of tubes, 26th International Congress and Exhibition on Computer Assisted Radiology and Surgery
(CARS), International Journal of CARS; 7 (S1):S79-S80, 2012.
23. C. Sci, D. Bainbridge, J. Moore, C. Wedlake, G. Guiraudon, D.L. Jones, T.M. Peters, Real-time 4D ultrasound
reconstruction for improved intraoperative imaging during image-guided beating-heart interventions, 24th International
Congress and Exhibition on Computer Assisted Radiology and Surgery (CARS), International Journal of CARS;
5(S1):S271-S273, 2010.
Won International Society for Computer Aided Surgery (ISCAS) Best Student Poster award.
24. C.A. Linte, D.S. Cho, M. Carias, C. Sci, J. Moore, C. Wedlake, D. Bainbridge, B. Kiaii, T.M. Peters, Estimating heart
movement and morphological changes during robot-assisted coronary artery bypass graft interventions, 24th International
Congress and Exhibition on Computer Assisted Radiology and Surgery (CARS), 2010.
25. C. Sci, T. Bui, P.K. Rose, Computational estimates of the effect of asynchronous synaptic activity on fluctuations in the
membrane potential of motoneurons, Society for Neuroscience (SfN), 2006.
BOOKS AND PROCEEDINGS
26. M.A. Zuluaga, K. Bhatia, B. Kainz, M.H. Moghari, C. Sci (eds). Reconstruction, segmentation and analysis of
medical images, First International Workshops, RAMBO 2016 and HVSMR 2016. LNCS 10129, 2016.
THESES
27. C. Sci
Image segmentation for highly variable anatomy: Applications to congenital heart disease.
Ph.D. Thesis. Cambridge, MA, USA: Massachusetts Institute of Technology, June 2020.
28. C. Sci
Real-time 4D ultrasound reconstruction for image-guided intracardiac interventions.
M.E.Sc. Thesis. London, ON, Canada: The University of Western Ontario, March 2010.
CONFERENCE PRESENTATIONS
• Iterative segmentation from limited training data: Applications to congenital heart disease, MICCAI Workshop on Deep
Learning in Medical Image Analysis, Granada, Spain, September 20, 2018 (poster).
• Challenge overview: Clinical motivation, data and evaluation, MICCAI Workshop on Whole-Heart and Great Vessel
Segmentation from 3D Cardiovascular MRI in Congenital Heart Disease, Athens, Greece, October 17, 2016 (oral).
• Interactive whole-heart segmentation in congenital heart disease, Medical Image Computing and Computer Assisted
Interventions (MICCAI), Munich, Germany, October 7, 2015 (poster).
• Creating 3D heart models of children with congenital heart disease using magnetic resonance imaging, International
Society for Magnetic Resonance in Medicine (ISMRM), Toronto, ON, Canada, June 2, 2015 (electronic poster).
• TubeTK: An open-source toolkit of algorithms operating on images of tubes, 26th International Congress and Exhibition
on Computer Assisted Radiology and Surgery (CARS), Pisa, Italy, June 2012 (oral).
• Sliding geometries in deformable image registration, MICCAI Workshop on Computational and Clinical Applications in
Abdominal Imaging, Toronto, ON, Canada, September 18, 2011 (oral).
• Deformable image registration of sliding organs using anisotropic diffusive regularization, International Symposium on
Biomedical Imaging (ISBI), Chicago, IL, USA, March 30, 2011 (oral).
• Real-time 4D ultrasound reconstruction for improved intraoperative imaging during image-guided beating-heart
interventions, 24th International Congress and Exhibition on Computer Assisted Radiology and Surgery (CARS), Geneva,
Switzerland, June 2010 (poster).
Won International Society for Computer Aided Surgery (ISCAS) Best Student Poster award.
• An open-source real-time ultrasound reconstruction system for four-dimensional imaging of moving organs, MICCAI
Workshop on Systems and Architectures for Computer Assisted Intervention, London, UK, September 24, 2009 (oral).
• Validation of four-dimensional ultrasound for targeting in minimally-invasive beating-heart surgery, SPIE Medical
Imaging, Lake Buena Vista, FL, USA, February 10, 2009 (oral).
• An accessible, hands-on tutorial system for image-guided therapy and medical robotics using a robot and open source
software, MICCAI Workshop on Open Source and Open Data, Brisbane, Australia, November 2, 2007 (oral).
• Computational estimates of the effect of asynchronous synaptic activity on fluctuations in the membrane potential of
motoneurons, Society for Neuroscience (SfN), Atlanta, GA, USA, October 14, 2006 (oral).
REGIONAL WORKSHOP PRESENTATIONS
• Whole heart segmentation in congenital heart disease by learning iterative segmentation, Boston Imaging Workshop,
Cambridge, MA, USA, November 15, 2019.
• Whole heart segmentation in congenital heart disease by learning iterative segmentation, Institute for Medical
Engineering and Science Industrial Group Symposium, MIT, Cambridge, MA, USA, October 3, 2019.
• Learning to create 3D-printed heart models for surgeons to treat congenital heart disease, College of Computing Launch,
MIT, Cambridge, MA, USA, February 28, 2019.
• Iterative segmentation from limited training data: Applications to congenital heart disease, New England Computer Vision
Workshop, Cambridge, MA, USA, November 26, 2018.
Won Best Presentation award.
• Four-dimensional echocardiography for minimally-invasive surgery on the beating heart, London Imaging Discovery,
London, ON, Canada, June 12, 2009.
• Accuracy of four-dimensional ultrasound for intraoperative imaging in minimally-invasive surgery on the beating heart, 7th
Imaging Symposium, Imaging Network Ontario, Toronto, ON, Canada, 2008.
Won 1st Poster in Imaging for Cardiovascular Therapeutics award.
• Initial model selection for the Baum-Welch algorithm as applied to HMMs of DNA sequences, Canadian Student
Conference on Biomedical Computing, Kingston, ON, Canada, March 2006 (* contributed equally).
Won Best Undergraduate Contribution award.
• Computational modeling of the effect of synaptic activity on fluctuations in the membrane potential of motoneurons,
Canadian Student Conference on Biomedical Computing (CSCBC), Kingston, ON, Canada, March 2006.
INVITED TALKS
• Whole heart segmentation in congenital heart disease by learning iterative segmentation, A.A. Martinos Center for
Biomedical Imaging, Charlestown, MA, USA, February 26, 2020.
• Image segmentation for highly variable anatomy: Applications to Congenital Heart Disease, Philips Research, Hamburg,
Germany (virtual), August 18, 2020.
• Whole heart segmentation in congenital heart disease by learning iterative segmentation, ETH Zurich, Zurich,
Switzerland, October 10, 2019.
• Whole heart segmentation in congenital heart disease by learning iterative segmentation, TU Munich, Munich, Germany,
May 24, 2019.
• Whole heart segmentation in congenital heart disease by learning iterative segmentation, Graphics Lunch Seminar
Series, MIT, Cambridge, MA, USA, December 18, 2019.
• Iterative segmentation from limited training data: Applications to congenital heart disease, Brigham and Women’s
Machine Learning / Deep Learning Journal Club, Cambridge, MA, USA, August 10, 2018.
• Interactive whole-heart segmentation in congenital heart disease, Kitware Inc., Carrboro, NC, USA, July 3, 2017.
• Interactive whole-heart segmentation in congenital heart disease, Philips Research, Hamburg, Germany, June 21, 2017.
• Sliding geometries in deformable image registration via locally-adaptive regularization, Robarts Research Institute,
London, ON, Canada, June 16, 2011.
• Registration and resampling using Brainsfit: Rigid, affine and non-rigid, Slicer Workshop, Biomedical Imaging Research
Centre, The University of Western Ontario, London, ON, Canada, June 15, 2011.
• Introduction to navigation using OpenIGTLink (I/O to trackers, devices and scanners: OpenIGTLink), NA-MIC Kit
Software Workshop, Robarts Research Institute, London, ON, Canada, October 16, 2008.
• MR-guided prostate interventions using the NA-MIC Kit (MR-guided prostate interventions), NA-MIC Kit Software
Workshop, Robarts Research Institute, London, ON, Canada, October 16, 2008.
• Planning for image-guided neurosurgery (IGT workflows using neurosurgical planning as an example), NA-MIC Kit
Software Workshop, Robarts Research Institute, London, ON, Canada, October 15-16, 2008.
• Image-guided therapy and medical robotics using a LEGO Mindstorms NXT robot and 3D Slicer (Lego robot tutorial),
NA-MIC Kit and Slicer3 User/Developer Workshop, Munich, Germany, June 17, 2008.
• Introduction to navigation using OpenIGTLink (I/O to trackers, devices and scanners: OpenIGTLink), NA-MIC Kit and
Slicer3 User/Developer Workshop, Munich, Germany, June 17, 2008.
• Planning for image-guided neurosurgery (IGT workflows), NA-MIC Kit and Slicer 3 User/Developer Workshop, Munich,
Germany, June 17, 2008.
• An accessible, hands-on tutorial system for image-guided therapy and medical robotics using a robot and open-source
software, Intelligent-OR Seminar, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan,
October 2007.
