Jason M. Samonds, PhD

email

412-268-3922 (office)

412-268-5060 (fax)

http://www.cnbc.cmu.edu/~samondjm/

 

Curriculum Vitae

 

 

OBJECTIVE

 

My motivation as a neuroscientist is to understand how cortical networks within and between early visual areas learn scene statistics and perform statistical inference functions such as complex and invariant pattern recognition, scene segmentation, and stereo correspondence.
 
CAREER EXPERIENCE

 

Postdoctoral Fellow

Carnegie Mellon University, Center for the Neural Basis of Cognition

January 2005 - present (supervisor: Tai Sing Lee, PhD)

 

My primary research goal is to test hypotheses about potential neurophysiological mechanisms of statistical inference among networks of V1 and V2 neurons. I use chronically implanted 100-electrode silicon arrays and the 32-electrode Gray Matter microdrive chamber system that allow me to record from populations of neurons in areas V1 through V4 in awake, behaving macaques over a period of years. I mentor and supervise other post-docs, graduate students, and undergraduate students majoring in computer science, engineering, and neuroscience. My work is presented in seminars and conferences as lectures and posters, and published for both general and neuroscience audiences. I give lectures in graduate and undergraduate classes on visual neuroscience and signal processing topics. One of my own NIH proposals was funded and I have helped write and develop several other funded proposals in the laboratory from a variety of funding sources, including the NIH, NSF, and Air Force. I learned the associated surgical procedures, as well as anesthesia and physiological monitoring for electrophysiological recordings from visual cortex of macaques.

 

Grant Support:

NIMH IBSC MH64445--------(James L McClelland) Interactive processes in perception (Tai Sing Lee and Carl Olson)

NSF CISE IIS-0413211------Statistical and neural basis of 3D surface inference in vision (Tai Sing Lee)

NSF CISE IIS-0713206------Computational and Neurophysiological Investigation of Robust Visual Inference (Tai Sing Lee)

NEI F32 EY017770-----------Spatial Integration of V1 Horizontal Disparity Signals (Jason Samonds)

AFOSR FA9550-09-1-0678--Multi-cue surface representation (Tai Sing Lee & Christopher Tyler)

NEI R01 EY022247----------- Neural representation of hierarchical visual concepts in natural scenes (Tai Sing Lee & Alan Yuille)

 

Postdoctoral Fellow

Vanderbilt University, Department of Electrical Engineering and Computer Science

May 2004 - January 2005 (supervisor: AB Bonds, PhD)

 

My research goal for this appointment was to test hypotheses about the role of cooperative neuronal interactions in detecting contours. I collected data from electrophysiological recordings from the 100-electrode Bionics Technologies array in primary visual cortex of anesthetized cats. I mentored and supervised graduate students and undergraduate students majoring in computer science and engineering. I presented my work in seminars and conferences as lectures and posters, and published my work, for both general and neuroscience audiences.

 

Grant Support:

NEI RO1 EY014680----------Representation of Visual Information in Striate Cortex (AB Bonds)

 

Research Assistant

Vanderbilt University, Department of Biomedical Engineering

May 1999 - May 2004 (supervisor: AB Bonds, PhD)

 

My thesis proposal was to examine the dynamics of spatiotemporal properties of the spiking responses of populations of neurons in the primary visual cortex. I implemented, designed, and maintained stimuli, data collection, and data analysis systems on PC, Sun Microsystems, and custom hardware. I developed and implemented a broad range of neural signal processing tools with an emphasis on probabilistic signal processing. I implemented and maintained 100- and 25-electrode Bionics Technologies microelectrode arrays for large scale multi-unit recordings. I helped with the successful formulation and submission of an NIH grant (NEI RO1 EY014680). I presented my work in seminars and conferences as lectures and posters, and published my work, for both general and neuroscience audiences. I learned the associated surgical procedures, as well as anesthesia and physiological monitoring for acute electrophysiological recordings from visual cortex of cats.

 

Grant Support:

NEI RO1 EY03778-----------Spatial Characteristics of Cells in the Striate Cortex (AB Bonds)

NEI RO1 EY014680----------Representation of Visual Information in Striate Cortex (AB Bonds)

 

 

 

Research Technician

Medical College of Wisconsin, Functional Imaging Research Center

May 1998 - May 1999 (supervisor: Thomas E Prieto, PhD)

 

I designed mechanical and electrical subject interface systems, and maintained these systems, for functional magnetic resonance imaging studies. My projects included audio and visual stimuli, feedback and response systems, and head restraint.

 

Grant Support:

NIH P01 MH51358----------(James S Hyde) Subject Interface Systems (Thomas E Prieto)

 

EDUCATION

 

Vanderbilt University, Nashville TN

 

Doctor of Philosophy in Biomedical Engineering, May 2004

Vanderbilt University, Nashville TN

Spatiotemporal analysis of synchronization of neural ensembles for spatial discriminations in cat striate cortex. Vanderbilt University PhD Dissertation, 2004. (pdf)

 

Master of Science in Biomedical Engineering, May 2002

Vanderbilt University, Nashville TN

Spike train analysis of spatial discriminations and functional connectivity of pairs of neurons in cat striate cortex. Vanderbilt University MS Thesis, 2002. (pdf)

 

G.P.A. 3.44(4.0)
Curriculum: Real-time Systems, Bioelectrical Signals, DSP, Artificial Intelligence, Neural Networks, Morphological Image Processing, Medical Imaging, Excitable Membranes, Visual System.

Workshops: NIPS Spike Train Analysis, UC-Berkeley BioMEMS

 

Research Assistantship, Academic Scholarship, Graduate School Travel Awards, Student Paper Award

 

Milwaukee School of Engineering, Milwaukee WI

 

Bachelor of Science in Biomedical Engineering, May 1999

Senior Design: Heart Sound Simulator, Design Team Associate Project Manager

 

G.P.A. 3.69(4.0) Major G.P.A. 3.70(4.0)
Curriculum: Instrumentation, Imaging, Signals, Control Systems, Thermo/Fluids, Biomedical Design, Biomaterials.

Workshops: MCW fMRI Experiment Design & Issues

Alumni Association Student Achievement Award

M.S.O.E., Walton Foundation, and Pearl Noren Scholarships

 

PUBLICATIONS


Invited Talks:

 

Spatiotemporal analysis of synchronization of neural ensembles for spatial discriminations in cat striate cortex. Sloan-Swartz Center, Salk Institute for Biological Studies. La Jolla, CA. April 26, 2004. (slide show)

 

Neuronal Ensemble Recording in the Cat Primary Visual Cortex. Center for the Neural Basis of Cognition. Carnegie Mellon University. Pittsburgh, PA. July 23, 2004.

 

Evidence of cooperative and competitive mechanisms for stereo computation in macaque V1. Workshop: What role does spike synchrony or correlation play in sensory processing? Cosyne, The Canyons, Utah. February 26-27, 2007 (slide show)

 

Representations of scene statistics in the primary visual cortex for inferring binocular disparity. Brain Corporation. La Jolla, CA November 1, 2011 (pdf) (slide show)

 

Scene statistics represented in V1 recurrent networks help to infer binocular disparity. Center for Perceptual Systems. University of Texas at Austin. Austin, TX, February 9, 2015.

 

Workshops Organized:

 

Samonds JM, Smith MA. What role does spike synchrony or correlation play in sensory processing? Cosyne, The Canyons, Utah. February 26-27, 2007 (link)

 

Presentations:

Allison JD, Smith KR, Atherton ME, Samonds JM, Bonds AB. Temporal frequency tuning of cross orientation inhibition in the striate cortex of cats. [ARVO abstr] Invest Ophthalmol Vis Sci, 2000. (abstract) (poster) (related article)

Brown HA, Allison JD, Samonds JM, Bonds AB. Nonlocal origin of response supression from stimulation outside the Classic Receptive Field in Area 17 of the cat. [VSS abstr] J Vision 1(3):200a, 2001. (abstract)

Brown HA, Allison JD, Samonds JM, Bonds AB. Area 18 contribution to spatial integration of receptive fields of area 17 cells in the cat. [VSS abstr] J Vision 2(7):582a, 2002. (abstract)

Samonds JM, Allison JD, Brown HA, Bonds AB. Spike train analysis reveals cooperation between Area 17 neuron pairs that enhances fine discrimination of orientation. [VSS abstr] J Vision 2(7):196a, 2002. (poster) (abstract)

 

Bonds AB, Samonds JM, Allison JD. Spike train analysis reveals cooperation between Area 17 neuron pairs that enhances fine discrimination of orientation. Annual Meeting of the Society for Mathematical Psychology, 2002. (slide show) (abstract)

Brown HA, Allison JD, Samonds JM, Thomas AM, Bonds AB. Characterization of area 18 modulation from stimulation outside the receptive field of area 17 cells in the cat. [VSS abstr] J Vision 3(9):373a, 2003. (abstract)

Samonds JM, Allison JD, Brown HA, Bonds AB. Cooperative Synchronized Assemblies and Orientation Discrimination. [VSS abstr] J Vision 3(9):152a, 2003. (slide show) (abstract)

 

Brown HA, Samonds JM, Bonds AB. Area 18 contributes to contrast adaptation of Area 17 cells in the cat. [VSS abstr] J Vision 4(8):224a, 2004. (abstract)

 

Samonds JM*, Brown HA, Bonds AB. Relationships between the spatiotemporal spike train structure and cortical synchronization. [VSS abstr] J Vision 4(8):17a, 2004. (slide show) (abstract)

*Student Travel Award

 

Samonds JM, Bonds AB. Quantitative analysis of cooperation and structure in the cat striate cortex. Workshop on Coding of Visual Information in the Brain, Isle of Skye, Scotland, 2004. (abstract) (paper)

 

Zhou Z*, Samonds JM, Bernard MR, Bonds AB. Synchronous activity in cat visual cortex encodes collinear and cocircular contours. [VSS abstr] J Vision 5(8):675a, 2005. (poster) (abstract)

*Student Travel Award

 

Bernard MR, Samonds JM, Zhou Z, Bonds AB. An integration model of detection and quantification of synchronous firing within cell groups. [VSS abstr] J Vision 5(8)676a, 2005. (poster) (abstract)

 

Samonds JM*, Potetz B, Lee TS. Cooperative processing of spatially distributed disparity signals in macaque V1. [VSS abstr] J Vision 6(6):831a, 2006. (slide show) (abstract)

*Student Travel Award

 

Potetz BR, Samonds JM, Lee TS. Disparity and luminance preference are correlated in macaque V1, matching natural scene statistics. [Soc Neurosci abstr], 2006. (slide show) (abstract)

 

Samonds JM, Potetz BR, Lee TS. Evidence of cooperative and competitive mechanisms for stereo computation in macaque V1. [Soc Neurosci abstr], 2006. (poster) (abstract)

 

Samonds JM, Potetz BR, Lee TS. Neurophysiological Evidence of Cooperative Mechanisms for Stereo Computation. [NIPS], 2006. (poster)

 

Samonds JM, Potetz BR, Lee TS. Evidence of cooperative and competitive mechanisms for stereo computation in macaque V1. OIST Workshop on Cognitive Neurobiology, Onna Village, Okinawa, Japan, 2007. (poster) (abstract)

 

Samonds JM, Potetz BR, Lee TS. Implications of neuronal interactions on disparity tuning in V1. [Soc Neurosci abstr], 2007. (poster) (abstract)

 

Samonds JM, Potetz BR, Poplin RE, Lee TS. Neuronal interactions reduce local feature uncertainty. [Soc Neurosci abstr], 2008. (poster) (abstract)

 

Samonds JM, Poplin RE, Lee TS. Binocular disparity in the surround biases V1 responses to ambiguous binocular stimuli within the classical receptive field. [Soc Neurosci abstr], 2009. (poster) (abstract)

 

Poole B, Lenz I, Lindsay G, Samonds JM, Lee TS. Connecting scene statistics to probabilistic population codes and tuning properties of V1 neurons. [Soc Neurosci abstr], 2010. (abstract)

 

Samonds JM, Poole B, Lee TS. V1 interactions reduce local uncertainty about binocular disparity over time. [Soc Neurosci abstr], 2010. (slide show) (abstract)

 

Lindsay G, Poole B, Doiron B, Samonds JM, Lee TS. Quality of tuning curves and their effect on population coding. [Cosyne], 2011. (abstract)

 

Samonds JM, Potetz BR, Tyler CW, Lee TS. Dynamics of binocular disparity tuning explained by a neural network model with recurrent interactions. [Soc Neurosci abstr], 2011. (poster) (abstract)

 

Samonds JM, Li X, Tyler CW, Lee TS. Neuronal interactions in area V2 and their role in stereoscopic three-dimensional shape processing. [Soc Neurosci abstr], 2012. (poster) (abstract)

 

Li X, Samonds JM, Lui Y, Lee TS. Pairwise interaction of V1 disparity neurons depends on spatial configural relationship between receptive fields as predicted by 3D scene statistics. [Soc Neurosci abstr], 2012. (poster) (abstract)

 

Samonds JM, Potetz BR, Tyler CW, Lee TS. Stereoscopic surface disambiguation and interpolation in the macaque primary visual cortex. [Cosyne], 2014. (poster) (abstract)

*Travel Award

 

Samonds JM, Li Y, Zhang Y, Lee TS. Late responses of V2 neurons are enhanced by global scene context of natural movies. [Soc Neurosci abstr], 2014. (poster)

 

Zhang Y, Li X, Samonds JM, Poole B, Lee TS. Relating functional connectivityin V1 neural circuits and 3D natural scenes using Boltzmann machines. [Cosyne], 2015.


Peer-reviewed Articles:

Brown HA, Allison JD, Samonds JM, Bonds AB. Nonlocal origin of response suppression outside of the classical receptive field in Area 17 of the cat.
Vis Neurosci 20(1):85-96, 2003. (pdf)

Samonds JM, Allison JD, Brown HA, Bonds AB. Cooperation between Area 17 neuron pairs enhances fine discrimination of orientation. J Neurosci 23(6):2416-2425, 2003. (pdf)

*Reviewed by the Faculty of 1000

 

Samonds JM, Allison JD, Brown HA, Bonds AB. Cooperative synchronized assemblies enhance orientation discrimination. Proc Nat Acad Sci USA 101(17):6722-6727, 2004. (pdf) (Daily Register) (Engineering News)

 

Samonds JM, Bonds AB. From another angle: Differences in cortical coding between fine and coarse discrimination of orientation. J Neurophysiol 91(3):1193-1202, 2004. (pdf)

 

Samonds JM, Bonds AB. Real-time visualization of neural synchrony for identifying coordinated cell assemblies. J Neurosci Meth 139(1):51-60, 2004. (pdf) (link)

 

Samonds JM, Bonds AB. Gamma oscillation maintains stimulus structure-dependent synchronization in cat visual cortex. J Neurophysiol 93(1):223-236, 2005. (pdf)

 

Samonds JM, Zhou Z, Bernard MR, Bonds AB. Synchronous activity in cat visual cortex encodes collinear and cocircular contours. J Neurophysiol 95(4):2602-2616, 2006. (pdf)

*Reviewed by the Faculty of 1000

 

Samonds JM, Potetz BR, Lee TS. Neurophysiological Evidence of Cooperative Mechanisms for Stereo Computation. Advances in Neural Information Processing Systems 19, MIT Press, 2007. (pdf)

 

Samonds JM, Potetz BR, Lee TS. Cooperative and competitive interactions facilitate stereo computations in macaque primary visual cortex. J Neurosci 29(50):15780-15795, 2009. (pdf)

 

Samonds JM, Potetz BR, Lee TS. Relative luminance and binocular disparity preferences are correlated in macaque V1, matching natural scene statistics. Proc Nat Acad Sci USA 109(16):6313-6318, 2012. (pdf)

 

Samonds JM, Potetz BR, Tyler CW, Lee TS. Recurrent connectivity can account for the dynamics of

disparity processing in V1. J Neurosci 33(7):2934-294, 2013. (pdf)

*Reviewed by Read J, Allenmark F. Visual perception: one world from two eyes. Curr Biol 23(11):R483-R486, 2013. (pdf)

 

Samonds JM, Potetz BR, Lee TS. Sample skewness as a statistical measurement of neuronal tuning sharpness. Neural Comp 26(5):860-906, 2014. (pdf)

 

Li X, Samonds JM, Lui Y, Lee TS. Neural circuits predicted by 3D natural scenes match the functional networks in V1. (under review) 2015.

 

Samonds JM, Tyler CW, Lee TS. Evidence of stereoscopic surface disambiguation and interpolation in the responses of V1 neurons. (under review) 2015.

 

Zhang Y, Li X, Samonds JM, Poole B, Lee TS. Relating functional connectivity in V1 neural circuits and 3D natural scenes using Boltzmann machines. (under review) 2015.

 

Samonds JM, Lee TS, Kuhlmann S. Non-uniform surround modulation enhances orientation tuning for neurons in mouse primary visual cortex. (in preparation) 2015.

 

Samonds JM, Li Y, Zhang Y, Lee TS. The effect of adaptation on surround modulation for macaque V2 neurons. (in preparation) 2015.

 

Lindsey G, Poole B, Samonds JM, Lee TS. Neural encoding of scene statistical priors. (in preparation) 2015.

 

Reviews and Commentary:

 

Samonds JM and Bonds AB. Cooperative and temporally structured information in the visual cortex. Signal Processing, 85(11):2124-2136, 2005. (pdf)

 

Samonds JM. Feature configuration modulates effective connectivity. J Neurosci 26(14):3621-3623, 2006. (pdf)

 

Kelly RC, Smith MA, Samonds JM, Kohn A, Bonds AB, Movshon JA, Lee TS. Comparison of recordings from microelectrode arrays and single electrodes in visual cortex. J Neurosci 27(2):261-264, 2007. (pdf) (cover)

 

Book Chapters:

 

Lee TS, Stepleton T, Potetz B, Samonds JM. Neural coding of scene statistics for surface and object inference In Object Categorization: perspectives from human and machine vision, Ed. Sven Dickinson, Ales Leonardis, Bernt Schiele, Michael Tarr, Cambridge University Press, 2008. (pdf)

 

Samonds JM, Lee TS. Neuronal interactions and their role in solving the stereo correspondence problem, In Vision in 3D Environments, Ed. Laurence Harris, Michael Jenkin, Cambridge University Press, 2011. (pdf)

 

Invited Reviewer:

 

Journal of Neuroscience

Journal of Neurophysiology

PLOS Computational Biology

European Journal of Neuroscience

Journal of Computational Neuroscience

Network: Computation in Neural Systems

Journal of Neuroscience Methods

Vision Research

Journal of Vision

Behavioral and Brain Functions

Signal Processing

 

AFFILIATIONS

 

Society for Neuroscience

American Physiological Society

Visual Sciences Society

Association for Research in Vision & Opthalmology

Institute for Electrical and Electronics Engineers

Engineering in Medicine and Biology Society

Biomedical Engineering Society

Tau Omega Mu Honor Society

 

 

 

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