Rick Giuly
Data Scientist, Sr. Software Engineer
San Diego, CA

Current Projects:
Sr. Engineer and Data Scientist at MDQ (Med Data Quest) Startup
Founder of AISings Music Generator (aisings.com)


Extensive experience with designing systems related to machine learning and data driven modeling. I have experience with both modeling and interface design. Currently I'm working with the startup company Med Data Quest to develop tools for automated medical diagnosis. My past experience includes leading efforts at the National Center for Medical Imaging Research to develop web based tools for training and testing models designed to detect and segment features in 3D images.

Technical Interests:
• Automatic segmentation and annotation of 3D biological data
• Mining "big data" with machine learning techniques
• Neural circuit reconstruction
• Large scale biologically realistic models of neural systems
• Connectomics

My view is that the history of medicine and medical technology shows a continuous gradual improvement from primitive practices thousands of years ago in Egypt up to the most advanced technology today. A new frontier in medical technology is development of medical technology to treat brain disease and nervous system damage. The brain is the most complex and important organ of a human body, but the least understood. Medical technology stems first from understanding, then from technology developed around that understanding.

Past Projects

  • Leading image data mining efforts at National Center for Imaging and Microscopy Research using machine learning and crowd sourcing to extract complex features from "big data" on the multi-terabyte scale. (2013)
  • The goal of the Cytoseg project is to produce a tool for automatic segmentation of 3D biological datasets, with emphasis on 3D electron microscopy. The project is written in Python and uses the pythonxy platform (which includes scipy and ITK image processing tools). Cytoseg is currently in a pre-alpha stage. (2010)
  • Masters's Thesis, Bioengineering, UCSD: Design and testing of a new conical beam precession system for high-throughput electron tomography (2008)
  • A System for Studying Brain-Body Evolution of Virtual Creatures (2004)

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 [related blog article]

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

Semi-Automated Neuron Boundary Detection and Nonbranching Process Segmentation in Electron Microscopy Images
Elizabeth Jurrus, Shigeki Watanabe, Richard J. Giuly, Antonio R. C. Paiva, Mark H. Ellisman, Erik M. Jorgensen and Tolga Tasdizen, Neuroinformatics 2012

Semi-automated Neuron Boundary Detection and Nonbranching Process Segmentation in Electron Microscopy Images

Elizabeth Jurrus, Shigeki Watanabe; Richard J Giuly; Antonio R. C. Paiva; Mark H. Ellisman; Erik M. Jorgensen; Tolga Tasdizen, Neuroinformatics 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, MICCAI 2011

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

Grant Sections

Contributed the 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.


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

A System for Studying Brain-Body Evolution of Virtual Creatures

Genetic and Evolutionary Computation Conference (GECCO), 2004
R. Giuly