Science and Engineering Resume

Richard J Giuly

Education

University of California, San Diego (2005-2008)

Degree: MS in Bioengineering

Special Courses

Numerical Methods for Science and Engineering

Algorithm Design and Analysis

Advanced BioPhotonics

Comparative Biomedical Imaging

Georgia Institute of Technology (Spring 2001 - Spring 2004)

Degree: BS in Computer Science with Highest Honor

Specialization: Intelligent Systems

Special Courses

Intelligent Systems

Transmission Electron Microscopy, graduate level

Introduction to MEMS, graduate level

Circuit Analysis

Journal Publications

DP2: Distributed 3D Image Segmentation Using Micro-labor Workforce, Richard J. Giuly*, Keun-Young Kim and Mark H. Ellisman, Bioinformatics, Oxford Journals, 2013

Method: Automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets, Richard J Giuly, Maryann E Martone and Mark H Ellisman, BMC Bioinformatics 2012

Detection of Neuron Membranes in Electron Microscopy Images Using Multi-scale Context and Radon-Like Features

Mojtaba Seyedhosseini, Ritwik Kumar, Elizabeth Jurrus, Rick Giuly, Mark Ellisman, Hanspeter Pfister and Tolga Tasdizen

Pro-hormone Secretogranin II Regulates Dense Core Secretory Granule Biogenesis in Catecholaminergic Cells

Maïté Courel, Alex Soler-Jover, Juan L. Rodriguez-Flores, Sushil K. Mahata, Salah Elias, Maïté Montero-Hadjadje, Youssef Anouar, Richard J. Giuly, Daniel T. O'Connor, Laurent Taupenot

A lithographically-patterned, elastic multi-electrode array for surface stimulation of the spinal cord

Kathleen W. Meacham*, Richard J. Giuly*, Liang Guo, Shawn Hochman, Stephen P. DeWeerth

Biomed Microdevices, 2008

A simple method for generating nano-pillars and uniformly separated nano-needle arrays on silicon

Richard J. Giuly, James L. Gole

Materials Letters, 2008

A PDMS-based Elastic Multi-Electrode Array for Spinal Cord Surface Stimulation and Its Electrode Modification to Enhance Performance

L Guo, KK Williams, RJ Giuly, SP DeWeerth

Abstracts and Conference Proceedings

Automatic Segmentation of Mitochondria Using Image Patch and Contour Classification

Bioimage Informatics, 2010

Rick Giuly, Maryann Martone, Mark Ellisman

Automatic detection and segmentation of membrane-stained subcellular components

R. Giuly, S. Lamont, M. Martone, M. Ellisman

Society for Neuroscience Annual Conference, 2009

Guo, L., K. K. Williams, Giuly, R. J., DeWeerth, S. P. (2006). "A PDMS-based Elastic

Multi-Electrode Array for Spinal Cord Surface Stimulation and Its Electrode

Modification to Enhance Performance [Presentation Highlights]." Solid-State Ionics 972.

A System for Studying Brain-Body Evolution of Virtual Creatures

Genetic and Evolutionary Computation Conference (GECCO), 2004

R. Giuly

Grant Sections

Wrote subcellular component automatic segmentation section to the Scalable Large Analytic Segmentation Hybrid (SLASH) RO1 Grant 1R01NS075314-01. Funded in 2011. PI's: Mark Ellisman and Tolga Tolga Tasdizen.

Wrote crowd based 3D segmentation section of IVEM and Image Analysis Resource grant awarded by NIH, 5P41GM103412-25, Contact PI / Project Leader: Ellisman, Mark H, UCSD

Collaborations

Currently collaborating with George Spirou's group, addressing 3D reconstruction of the developing Calyx of Held

Experience

Data Scientist and Sr. Software Engineer (2013 - present)

Med Data Quest - We're a startup company changing modern medical practice for the better by applying machine learning and natural language processing to electronic medical records. We're working with medical industry leaders including Kaiser Permanente.

· Accomplishments for first month: prototyped a web based interface for reviewing machine learning based predictions using Python, Django, and MySQL.

Advanced Automatic Segmentation Development (2008 - 2013)

· Developed software requirements for web based 3D image segmentation software

· Developed and published new method for automatic segmentation of subcellular structures addressing the need for more accurate and robust techniques to delineate structures in serial blockface scanning electron microscopic data.

· Coordinated project meetings between Scientific Computing and Imaging Institute at Utah University and National Center for Microscopy and Imaging Research (NCMIR)

Electron Tomography Technology Development (2006 - 2007)

National Center for Microscopy and Imaging Research (NCMIR)

Advisor: Mark Ellisman

· Developed imaging technology for high throughput transmission electron tomography. The goal of this technology is to acquire 3D volumetric images (on the order of 50mm3) at nanometer resolution. While this would have various uses in biology, it has a key application in the brain where understanding the ultrastructure requires submicron resolution and volumetric images that elucidate the way neurons are "wired" in 3D. For the past year I have been designing and testing a high speed control system for a new mode of electron tomography based on electron beam movement rather than the traditional method of mechanical stage rotation.

· Characterized the expected 3D reconstruction quality evaluating the effectiveness of Fourier transform based deconvolution with various electron beam sweep patterns.

Microfabricated Conformable Electrode Array (Fall 2004 - Spring 2005)

Emory Physiology Department and Georgia Tech Laboratory For Neuroengineering

Advisors: Prof. Shawn Hochman, Prof. Stephen DeWeerth

· Developed a safe, conformable, flexible microelectrode array to interface with the human spinal cord could enable electronic activation of spinal circuits that a person has lost control of from spinal cord injury. I designed, fabricated, and tested a novel conformable 2D microelectrode array for spinal cord stimulation. The project gave me an opportunity to gain practical experience in microfabrication and electrophysiology experimentation. Results for this project have been published in the journal Biomedical Microdevices.

Evolved Virtual Creatures (Fall 2003 - Spring 2004)

Georgia Tech College of Computing

Advisor: Prof. Tucker Balch

· Created an artificial life program where virtual creatures evolve in a physically simulated 3D environment. Given a user-defined fitness function, a genetic algorithm evolves the creature’s brain (an artificial neural network) and physical morphology based on its performance in simulation. My program successfully evolved creatures with walking and block pushing behavior. The project received second place at Georgia Tech’s undergraduate research symposium, and I presented it at the undergraduate workshop of the 2004 Genetic and Evolutionary Computation Conference. Images and videos are available at http://www.jungleboogie.org .

Nano-structure Research (Spring 2002 - Summer 2003)

Georgia Tech Physics Department

Advisor: Prof. James Gole

· Working with Prof. Gole’s group, I completed three special project courses and two summers funded by a Research Experience for Undergraduates (REU) program. I electrochemically etched porous silicon for gas sensor applications and designed an etching chamber to improve etching reproducibility. I also developed a method for electroless nickel deposition on nanoporous silicon to improve lithium ion battery capacity. I verified the method with scanning electron microscopy and energy dispersive X-ray analysis.

Molecular Dynamics (Fall 2002)

Georgia Tech Center for Experimental Research in Computer Systems

Advisor: Dr. Matthew Wolf

· For a special project course, I worked on integrating a network event delivery system, ECho, into an open source molecular dynamics program, VMD. I studied VMD’s C++ source code and modified it to accept information from an ECho data channel. The purpose of the project was to link VMD to Dr. Wolf’s visualization software via ECho and enable collaborative realtime interaction and remote visualization of molecular dynamics simulations.

Aerial Robotics Image Processing (Spring 2002)

Georgia Tech College of Computing

Advisor: Prof. James Rehg

· As a member of the Georgia Tech Aerial Robots Team, I created a graphical Java program for exploring onboard camera image processing algorithms, which helped our team win first place in the 2002 International Autonomous Aerial Robotics Competition. The program allowed us to test edge detection, Hough transforms, and custom feature extraction algorithms on various images.

Neural Feedback and Interpretation (Fall 2001)

Georgia Tech and Georgia State University

Advisor: Prof. Melody Moore

· Prof. Moore creates brain-computer interface software that gives severely paralyzed users the ability to control a computer with brain signals. I designed, programmed, and tested a biofeedback software application, BrainTrainer, to help patients visualize and control neural activity from a “neurotrophic” electrode. Prof. Moore continues to use BrainTrainer in her research.

Honors

· CRBS Staff Appreciation and Recognition award 2012

· Georgia Tech 2004 Undergraduate Research Symposium, 2nd Place Judges Award

· Graduated from Georgia Tech with Highest Honor

· Dean's list standing at VSU and GA Tech for 11 semesters and faculty honors Spring 2004

· Hope Scholarship

Memberships

· Society for Neuroscience

· Georgia Tech Aerial Robotics Team

· UPE International Honor Society for the Computing and Information Disciplines

· Golden Key International Honor Society

· American Association for the Advancement of Science

· Association for Computing Machinery

· American Association for Artificial Intelligence

· Georgia Tech Musician's Network

Technical Skills

Matlab, Python, Scipy, Linux, C, C++, Lisp, Django, ITK, OpenCV, Cubase