Curriculum Vitae  
Contact
Michal Sofka, PhD
Image Analytics and Informatics
Siemens Corporate Research
755 College Road East
Princeton, NJ 08540
USA

Email: Michal Sofka email

Links: Short bio, CV in PDF format

Research Interests
Vessel extraction in medical images, initialization for image registration, uncertainty and constraints in image registration, range data registration, and location registration and recognition.

Currently, I work at Siemens Corporate Research in the Department of Integrated Data Systems headed by Dr. Dorin Comaniciu.

Previously, I did my doctoral work with professor Chuck Stewart in the Computer Vision Group in the Department of Computer Science at RPI.

Education
Rensselaer Polytechnic Institute Troy, NY
Doctor of Philosophy, Computer Science August 2008
Master of Science, Computer Science May 2006
Union College Schenectady, NY
Master of Science, Electrical Engineering June 2001
Czech Technical University Prague, Czech Republic
Electrical Engineering (Undergraduate Student) 1996 - 1998, 1999 - 2000
Union College Schenectady, NY
Electrical Engineering (Exchange Student) 1998 - 1999
Industrial and Academic Experience
Siemens Corporate Research
Image Analytics and Informatics

Princeton, NJ
Project Manager 2011 - present
Managed research and development projects for various Siemens business units and external customers. Lead team of 4-6 members. Group Leader: Dorin Comaniciu.
Siemens Corporate Research
Image Analytics and Informatics

Princeton, NJ
Research Scientist 2008 - 2011
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.
Rensselaer Polytechnic Institute, Department of Computer Science Troy, NY
Research Assistant 2003 - 2008
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.
Rensselaer Polytechnic Institute, Department of Computer Science Troy, NY
Teaching Assistant 2001 - 2005 (4 semesters)
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.
SIEMENS Corporate Research, Department of Intelligent Vision and Reasoning Princeton, NJ
Temporary Technical Employee Jan. 2004 - Aug. 2004
Designed, analyzed, validated, and maintained algorithms for automatic composing of Magnetic Resonance Images and Angiograms. Supervised an undergraduate intern.
Union College, Department of Electrical Engineering Schenectady, NY
Union College, Department of Electrical Engineering 2000 - 2001
Tutored students; provided guidance on assignments; held review sessions; and helped students to master the coursework material. Computer assistant in the Curricular Support group.
Computer Vision Expertise

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).

Software Development Skills
  • 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).
  • 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).
  • Working knowledge of software engineering and collaborative product development of large projects, Concurrent Versions System (CVS), MS Visual SourceSafe, regression testing, nightly builds.
  • Familiar with scripting languages Perl, PhP, Bash.
Mentor and Supervisor

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

Professional Activities
Referee and Reviewer
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)
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
Co-Referee
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
Graduate Student Member
Institute of Electrical and Electronic Engineers (IEEE).
Publications and Research
Please see a separate page dedicated to publications and research projects.


 

Copyright 2012 Michal Sofka