Data Engineering

F ERNANDO A MAT

***** ***** **. *******, * *****

A +1-571-***-****; *****@*******.****.*** www.FernandoAmat.com

Education

Stanford University Stanford, CA Sept. 2004-June 2010

Ph.D. in Electrical Engineering with advisor Prof. Mark Horowitz and co-advisor Prof. Daphne Koller.

GPA: 3.9/4.0

Dissertation: Alignment of Cryo-Electron Tomography Images Using Markov Random FIelds

Center for Superior Interdisciplinary Education (CFIS) at

Technical University of Catalonia (UPC) Barcelona, Spain Sept. 1999-June 2004

Bachelor of Science, Telecommunication Engineering (5 year degree)

Graduated 4th out of 290 students

Bachelor of Science, Mathematics (5 year degree)

Graduated 2nd out of 31 students

Research Experience

Janelia Farm Research Campus-HHMI (Research Specialist) Ashburn, VA Sept. 2011 present

Janelia Farm Research Campus-HHMI (Research Associate) Ashburn, VA June 2010 Sept. 2011

Probabilistic models for large-scale image processing algorithms of microscopy images

Siemens Corporate Research-Integrated Data Systems (Intern) Princeton, NJ June Sept. 2007

Implemented semantic-based indexing of fetal anatomies from 3-D Ultrasound Data

Sharp Labs of America-Advanced Video & Display Technology (Intern) Camas, WA June Sept. 2005

Developed data-mining techniques on large datasets obtained from TV users

Robert Gordon Univ.-Food Science and Technology Lab (Intern) Aberdeen, Scotland June Sept. 2004

Developed mathematical models to measure food thermal properties

Univ. of Massachusetts-Microwave Remote Sensing Lab (Intern) Amherst, MA June Sept. 2003

Tested technique to measure cross-beam velocity with two X-Band antennae

Teaching Experience

Mission Day Care (Tutor) San Francisco, CA Feb. 2008 Aug. 2009

Volunteered on ve person team to help 60 at risk children aged 5 to 12 years

Stanford University (TA) Stanford, CA Sept. Dec. 2005

Prepared course materials, held of ce hours and gave lectures when professor was away

Stanford Disability Resource Center (Tutor) Stanford, CA Jan. June 2005

Tutored individual graduate level students in the School of Engineering

Casal del Raval dels Infants (Tutor) Barcelona, Spain June 2002 June 2003

Volunteered on seven person team to help 35 at risk children aged 3 to 8 years

Publications

F. Amat, E. Myers, and P.J. Keller, "Fast and robust optical ow for time-lapse microscopy using

super-voxels," Bioinformatics, submitted.

R. Tomer, K. Khairy, F. Amat, and P.J. Keller, "Quantitative high-speed imaging of entire developing embryos

with simultaneous multiview light-sheet microscopy," Nature Methods, vol. 9, no. 7, pp. 755-763, June 2012.

T. Zhao, J. Xie, F. Amat, N. Clack, P. Ahammad, H. Peng, and E. Myers, "Automated Reconstruction of

Neuronal Morphology Based on Local Geometrical and Global Structural Models," Neuroinformatics, vol. 9,

no. 2-3, pp. 247-261, May 2011.

K. Miyamichi, F. Amat, Farshid Moussavi, C. Wang, I. Wickersham, N. R. Wall, H. Taniguchi, B. Tasic, Z. J.

Huang, Z. He, E. M. Callaway, M.Horowitz, and L. Luo, "Cortical representations of olfactory input by

trans-synaptic tracing," Nature, vol. 472, no. 7342, pp. 191-196, Apr. 2011.

F. Amat, L. Comolli, J. Nomellini, F. Moussavi, K. H. Downing, J. Smith, and M. Horowitz, "Analysis of Intact

Surface Layer of Caulobacter crescentus by Cryo-Electron Tomography," Journal of Bacteriology, vol. 192, no.

22, pp. 747-757, Nov. 2010.

F. Amat, D. Casta o-Diez, A. Lawrence, F. Moussavi, H. Winkler, and M. Horowitz, "Alignment of

Cryo-Electron Tomography Datasets," in Cryo-EM, Part B: 3-D Reconstruction, vol. 482, Academic Press, pp.

343-367, Oct. 2010.

F. Amat, L. R. Comolli, F. Moussavi, J. Smit, K. H. Downing, and M. Horowitz, "Subtomogram alignment by

adaptive Fourier coef cient thresholding," Journal of Structural Biology, vol. 171, no. 3, pp. 332-344, Sep. 2010.

F. Moussavi, G. Heitz, F. Amat, L. R. Comolli, D. Koller, and M. Horowitz, "3D segmentation of cell

boundaries from whole cell cryogenic electron tomography volumes," Journal of Structural Biology, vol. 170,

no. 1, pp. 134-145, Apr. 2010.

S. Gould, F. Amat, and D. Koller, "Alphabet SOUP: A Framework for Approximate Energy Minimization," in

CVPR, pp. 903-910, June 2009.

G. Carneiro, F. Amat, B. Georgescu, S. Good, and D. Comaniciu, "Semantic-based indexing of fetal anatomies

from 3-D ultrasound data using global/semi-local context and sequential sampling," CVPR, pp. 1-8, June

2008.

F. Amat, F. Moussavi, L. R. Comolli, G. Elidan, K. H. Downing, and M. Horowitz, "Markov random eld

based automatic image alignment for electron tomography," Journal of Structural Biology, vol. 161, no. 3, pp.

260-275, March 2008.

Invited talks and oral presentations

(Invited talk) High-throughput image processing and cell lineage analysis pipeline for multi-view light sheet

microscopy. IEEE International Symposium on Biomedical Imaging. UNCC Bioinformatics Seminar Series.

Charlotte, USA, 2012

(Invited talk) High-throughput image processing and cell lineage analysis pipeline for multi-view light sheet

microscopy. IEEE International Symposium on Biomedical Imaging. The Krasnow Institute Seminar. Fairfax,

USA, 2012

(Invited lecturer) Fundamentals of subtomogram averaging. NCCR Workshop on Subtomogram Averaging. Basel,

Switzerland, 2012.

(Invited lecturer) Multivariant and multidimensional data analysis. Courses @CRG: Summer Course Modeling

for Systems Biology. Barcelona, Spain, 2012.

(Poster) High-throughput image processing and cell lineage analysis pipeline for multi-view light sheet

microscopy. IEEE International Symposium on Biomedical Imaging. Barcelona, Spain, 2012.

(Invited talk) Raptor 2.0: Alignment of Electron Tomography Datsets with ducial markers by maximum

likelihood. Sixth International Congress on Electron Tomography. Heidelberg, Germany, 2011.

(Talk) Gordon Research Conference on Three Dimensional Electron Microscopy. Lucca, Italy, 2010.

(Talk) Structural Analysis of Caulobacter Crescentus CB15 S-layer by Cryo-Electron Tomography of Whole

Cells. Asia-Paci c Congress on Electron Tomography. Brisbane, Australia, 2009.

(Invited workshop)Automated Tracking for Alignment of Electron Microscope Images. Tomography workshop.

San Diego, USA, 2008.

(Talk) Markov random eld based automatic image alignment for electron tomography. Advances in Neural

Information Processing Systems. Whistler, Canada, 2007.

(Invited workshop) EM Tomography Enhancements. Genomics: GTL Awardee Workshop V. Bethesda, USA, 2007.

(Poster) Automatic Projective Model Estimation And Reconstruction In Cryogenic Electron Tomography.

Sixth International Congress on Electron Tomography. San Diego, USA, 2006.

Patents

G. Carneiro, F. Amat, B. Georgescu, S. Good, and D. Comaniciu, "Automated Fetal Measurement from

Three-Dimensional Ultrasound Data." U.S. Patent 2009/0093717, issued April 9, 2009.

V. Kumar, F. Amat, "User Intent Prediction." U.S. Patent 2008/0228685, issued Sept. 18, 2008.

V. Kumar, F. Amat, "Method And System For Evaluating Media-playing Sets." U.S. Patent 2008/0183705,

issued July 31, 2008.

Skills and Interests

Language: Spanish (native), Catalan (native), English ( uent at all levels), German (beginner level)

Programing: pro cient in C++, Matlab, CUDA

Extra-curricular activities: avid traveler, cyclist and outdoorsman

Contact this candidate