Who Am I ?
Here is a presentation of my higher education : Classes and Research activities
Scientific Computing and Imaging Institute
The SCI research group was founded in 1994 by Drs. Chris Johnson and Rob MacLeod along with five graduate students.
The Scientific Computing and Imaging (SCI) Institute is now one of eight permanent research institutes at the University of Utah and home to over 200 faculty, students, and staff. The SCI Institute either directs or is associated with several national research centers: the NIH Center for Integrative Biomedical Computing (CIBC), the DoE Scalable Data Management, Analysis, and Visualization (SDAV), the NIH National Alliance for Medical Image Computing (NA-MIC), the DoE Scientific Data Management Center, the NIH Center for Computational Biology, and the DoE Center for the Simulation of Accidental Fires and Explosions (C-SAFE). In July, 2008, SCI was chosen as one of three NVIDIA Centers of Excellence in the U.S.
I started to work in Doctor Gerig's Medical Imaging Lab in July 2011. Dr Gerig is a recognized expert in neuroscience and Medical Imaging. His lab is composed of a dozen MS and PhD students working on challenging medical imaging issues.
My research is funded by various Grants from the National Institute of Health.
Research Projects
➟ Diffusion Tensor Imaging : Uncertainty quantization
Uncertainty Quantization in DTI Atlas Building Pipeline
➟ Quality Control
➟ Diffusion Tensor Imaging : Entropy and artifact assessment
➟ Brain Tractography
Explore neurons network
Tractography is a 3D modelling technique used to visually represent neural tracts using data collected by diffusion tensor imaging (DTI). Each local tensor contains the principal diffusion direction which is its larger eigenvector.
Longitudinal Analysis
Our data set contains several acquisition for each baby allowing us to explore the temporal evolution of diffusion properties such as Fractional Anisotropy
➟ Quality Control
➟ Large Data Set Visualization
➟ Atlas Building
Presentation and Seminars
➟ Medical Imaging Seminar
Presentation
➟ Utah Student Presentation
Presentation
➟ CPE Students Presentation
Presentation
University of Utah
During my first year as researcher at the SCI Institute, Dr Gerig offered me to stay one more year to keep working on cutting edge research projects and improve my skills and knowledge in Medical Imaging.
This year is my last year for my Master of Engineering at CPE Lyon.
Here is a presentation of the Classes I attended at the University of Utah.
Spring 2013
➟ 3D Computer Vision
3D Computer Vision CS6320
Project 1 : Camera Calibration. Mathematical Framework of Camera Calibration and practical applications.
Project 2 : Stereoscopy. Depth reconstruction, epipolar lines and points on a pair of images. Disparity map computation.
Projet 3 : Shape from Shading : Depth reconstruction using several light source. Lambertian surfaces and reflectance maps.
Projet 4 : Optical Flow and Structured Lighting : Motion estimation in video stream.
Project 5 : Multiple Baseline Stereo : Depth reconstruction based on translating camera. Reference : M. Okutomi, T. Kanade, A Multiple Baseline Stereo.
➟ Probabilistic Modeling
Probabilistic Modeling CS6957
This course focuses on how to use probability theory to model and analyze data. Data in the real world almost always involves uncertainty. This uncertainty may come from noise in the measurements, missing information, or from the fact that we only have a randomly sampled subset from a larger population. Probabilistic models are an effective approach for understanding such data, by incorporating our assumptions and prior knowledge of the world. These ideas are important in many areas of computer science, including machine learning, data mining, natural language processing, computer vision, and image analysis.
Topics : MLE, Bayesian Analysis, Prior distributions, Exponential Families, Maximum Entropy Priors, Multiparameter Models, Bayesian Linear Regression, Graphical Models and Bayesian Network, CMarkov random Fields, Monte Carlo Methods, Markov chain Monte Carlo, Gibbs Sampling.
➟ Medical Imaging Seminar
Medical Imaging Seminar CS7938
Research seminars from students, Faculty, PIs or international visitors.
Two amazing talks:
Daniel Rueckert, Imperial College London, UK : Machine learning meets medical Imaging
Fall 2012
➟ Image Processing
Image Processing CS6640
Project 2 : Filtering. Spatial filtering, Gaussian, edge detection, pattern matching.
Project 3 : Line dectection using Hough Transform.
Project 4 : Affine Registration, Radial Basis Functions Registration.
Project 5 : Active Contour : Snake using Calculus variations
➟ Scientific Visualization
Scientific Visualization CS6630
Project 1 : Information Visualization : Data Base analysis using "Tableau".
Project 2 : plot techniques using Processing programming language.
Project 3 : Parallel coordinate software developed with Processing.
Project 4 : 2D Spatial visualization using VTK and Python.
Project 5 : 3D Spatial visualization using VTK and Python.
Project 6 : Vector Field visualization using VTK et Python.
➟ Probabilities and Statistics
➟ Medical Imaging Seminar
Medical Imaging Seminar CS7938
Research seminars from students, Faculty, PIs or international visitors.
I gave a talk on Monday september 10th 2012 about DTI Artefacts.
Présentation
➟ Visualization Seminar
Visualization Seminar CS7942
Research seminars from students, Faculty, PIs or international visitors.
Fall 2012
➟ Riemannian Geometry
Introduction to Riemannian Manifolds CS7931
Riemannian Metrics, Affine and Riemannian Connections, Geodesics.
➟ Medical Imaging Seminar
Medical Imaging Seminar CS7938
Research seminars from students, Faculty, PIs or international visitors.
➟ Visualization Seminar
Visualization Seminar CS7942
Research seminars from students, Faculty, PIs or international visitors.
CPE Lyon
Suite à l'obtention avec mention en 2007 de mon baccalauréat Scientific Européen j'ai été admis sein des classes préparatoires de l'Institution des Chartreux à Lyon. J'ai fait ma première année de Maths supérieures en MPSI puis ma seconde année de Maths spéciales en PSI.
En 2009, après deux ans de classes préparatoires j'ai été admis dans le département Electronique Télécommunication et Informatique (ETI) de l'Ecole Supérieure de Chimie Physique et Electronique de Lyon (CPE Lyon).
Voici une présentation des cours que j'ai suivis à CPE Lyon entre 2009 et 2011
Second year
➟ Specialization
Image synthesis
Bresenham Algorithm, Graphical Rendering techniques, Phong Shading.
Computer Science and Mathematical modelling
sorting algorithm, "divide and conquer", mathematical morphology, Fractal Theory, Monte Carlo Method, Cellular automata, Lindemayer Systems, Logical Programming Prolog, Attractors.
Mathematical optimization
Simplexe, BFGS algorithm et KKT conditions.
Digital Filtering
FIR & IIR, implementation, structure, DSP.
➟ Core Scientific classes
Operating systems
basic UNIX functions, process management, multithread, semaphores.
Advanced Digital Electrical Systems
Digital functions, VHDL
Advanced Analog functions
Filtering, Phase Lock Loop, Analog Digital Conversion and Digital to Analog.
Microprocessor systems
Internal architecture and integration in complex systems.
Signal Processing
Filtering, signal processing, FFT, noise analysis.
➟ Other
Management
English
Spanish
First year
➟ Core Scientific classes
C/C++ Programming
Electrical Engineering
Signal Processing and Linear system analysis
Quantum mechanics
➟ Other
Company Creation contest : Electreecity
Award: Grand Prix Campus Création 2010
Economy
English
Spanish
BioClinica
Other Skills
Here are listed some skills I have
Computer Science
Programming Languages
C/C++, Linux Shell, tcsh, Python, Processing, Qt, HTML, CSS, SQL/MySQL, Cmake, Git, Mercurial, Matlab, R, ITK, VTK
Software
Microsoft office/Open Office, Matlab, web site and Databases management, Blender, LateX
Environment
Windows NT, Linux Ubuntu and OpenSuse, Mac OS X
Languages
French : native
English : Full Professional Proficiency (Cambridge First Certificate of English in 2007, TOIC in 2009 score 870), TOEFL iBT 109/120 (March 2012)
Spanish : Professional Proficiency
Reference
Joel Scharer PhD : Research supervisor at BioClinica
Guido Gerig PhD : Mentor at SCI Institute : 
Lettre de recommandation
Jean Marie Becker PhD : Mentor at CPE Lyon : 
Awards
Dean List Designation, University of Utah : 4.0 GPA
"Grand Prix Campus Création 2010" (Company Creation Contest)