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Contact
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Michal Sofka, PhD
Image Analytics and Informatics
Siemens Corporate Research
755 College Road East
Princeton, NJ 08540
USA
Email: 
Links: Short bio,
CV in PDF format 
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Research Interests
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Vessel extraction in medical images, initialization for image registration,
uncertainty and constraints in image registration, range data registration,
and location registration and recognition.
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Currently, I work at
Siemens Corporate Research
in the
Department of Integrated Data Systems headed by Dr.
Dorin Comaniciu.
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Previously, I did my doctoral work with professor
Chuck Stewart in the
Computer Vision Group
in the Department of Computer Science
at RPI.
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Education
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Rensselaer Polytechnic Institute
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Troy, NY
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Doctor of Philosophy, Computer Science
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August 2008
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Master of Science, Computer Science
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May 2006
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Union College
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Schenectady, NY
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Master of Science, Electrical Engineering
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June 2001
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Czech Technical University
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Prague, Czech Republic
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Electrical Engineering (Undergraduate Student)
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1996 - 1998, 1999 - 2000
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Union College
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Schenectady, NY
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Electrical Engineering (Exchange Student)
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1998 - 1999
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Industrial and Academic Experience
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Siemens Corporate Research
Image Analytics and Informatics
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Princeton, NJ
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Project Manager
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2011 - present
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Managed research and development projects for various Siemens business units and external customers.
Lead team of 4-6 members.
Group Leader: Dorin Comaniciu.
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Siemens Corporate Research
Image Analytics and Informatics
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Princeton, NJ
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Research Scientist
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2008 - 2011
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Developed a system for semantic indexing of ultrasound anatomies. Designed a learning-based
algorithm leveraging expert knowledge embedded in a large annotated database of medical images.
Group Leader: Dorin Comaniciu.
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Rensselaer Polytechnic Institute, Department of Computer Science
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Troy, NY
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Research Assistant
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2003 - 2008
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Implemented innovative and robust solutions to research problems
in the areas of retinal vessel extraction, uncertainty in point
and image registration, multimodal and illumination invariant
keypoint descriptors, and location registration and recognition
for mapping regions in CT scans. Published 8 papers and wrote
70K+ lines of C++ code. Supervised undergraduate research students.
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Rensselaer Polytechnic Institute, Department of Computer Science
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Troy, NY
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Teaching Assistant
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2001 - 2005 (4 semesters)
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Led labs of 60 students in 2 groups; graded and designed homework assignments, projects, and exams; held office hours; supervised exams; and provided help outside the class.
Served as a master TA the last semester.
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SIEMENS Corporate Research, Department of Intelligent Vision and Reasoning
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Princeton, NJ
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Temporary Technical Employee
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Jan. 2004 - Aug. 2004
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Designed, analyzed, validated, and maintained algorithms for automatic composing of Magnetic Resonance Images and
Angiograms. Supervised an undergraduate intern.
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Union College, Department of Electrical Engineering
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Schenectady, NY
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Union College, Department of Electrical Engineering
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2000 - 2001
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Tutored students; provided guidance on assignments; held review sessions; and helped students to master the coursework
material. Computer assistant in the Curricular Support group.
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Computer Vision Expertise
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Registration: Robust and automatic feature based registration
in the presence of physical and illumination changes, noise,
outliers, occlusions and missing structure; uncertainty
modeling for correspondence estimation; transformation
parameter covariance estimation; statistical models in image registration; multiresolution techniques;
piecewise affine deformable registration models.
Matching: Initialization of registration algorithms and feature analysis;
keypoint detectors, descriptors and matching; feature extraction and scale
space.
Segmentation: Matched filtering and intensity
Hessian based methods for the detection of linear features; vessel centerline
extraction; efficient vessel tracing.
Recognition: Location recognition, initialization of registration, automatic alignment verification.
Data: Experience with range data (LIDAR), visible spectrum and infra red (IR) imagery,
computed tomography (CT), magnetic resonance (MR) images and
angiograms (MRA).
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Software Development Skills
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Expert in C/C++ (multi-platform and compiler independent
development) with strong debugging and optimization skills;
proficient in Matlab (optimization, statistics, symbolic math and image
processing toolboxes, object oriented programming, vectorized
code).
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Skilled in integration with software libraries: Computer Vision
Libraries, VXL (since 2001), Insight
Toolkit, ITK (since 2004), Visualization
Toolkit, VTK (since 2006), Fast Light Toolkit, FLTK (since 2007),
RPI CS Computer Vision codebase (400k+ lines, C++; Administrator since
2001).
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Working knowledge of software engineering and collaborative product development of large projects,
Concurrent Versions System (CVS), MS Visual SourceSafe, regression testing, nightly
builds.
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Familiar with scripting languages Perl, PhP, Bash.
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Mentor and Supervisor
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Kristof Ralovich (Technical University Munich, Germany), 2009
Neil Birkbeck (University of Alberta, Canada), 2010
Jens Wetzl (University of Erlangen, Germany), 2010
Vimal Singh (University of Texas, Austin, TX, USA), 2011
Enrico Kuhn (Karlsruhe Institute of Technology, Germany), 2011
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Professional Activities
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Referee and Reviewer
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Journals:
IEEE Transactions on Medical Imaging (TMI)
IEEE Transactions on Image Processing (TIP)
Medical Image Analysis (MedIA) (Co-Referee)
IEEE Transactions on Biomedical Engineering (TBE)
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Conferences:
Computer Vision and Pattern Recognition (CVPR), 2009
European Conference on Computer Vision (ECCV), 2008
International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2008
IEEE Conference on Advanced Video and Signal based Surveillance (AVSS), 2008
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Co-Referee
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IEEE Computer Vision and Pattern Recognition (CVPR), 2008, 2007, 2006
European Conference on Computer Vision (ECCV), 2006
International Conference on Computer Vision (ICCV), 2005
International Conference on 3-D Digital Imaging and Modeling (3DIM), 2007
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Graduate Student Member
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Institute of Electrical and Electronic Engineers (IEEE).
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Publications and Research
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Please see a separate page dedicated to publications
and research projects.
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