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thesis.bib
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% This file was created with JabRef 2.10.
% Encoding: UTF-8
@Article{albrecht_jneurophys02,
Title = {{Visual Cortex Neurons of Monkeys and Cats: Temporal Dynamics of the Contrast Response Function}},
Author = {Albrecht, Duane G. and Geisler, Wilson S. and Frazor, Robert A. and Crane, Alison M.},
Journal = {Journal of Neurophysiology},
Year = {2002},
Month = {August},
Number = {2},
Pages = {888--913},
Volume = {88},
Day = {1},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/albrech_jnp02.pdf:PDF},
Keywords = {adaptation, coding, invariance, visual},
Pmid = {12163540},
Posted-at = {2007-12-19 14:22:52},
Url = {http://jn.physiology.org/cgi/content/abstract/88/2/888}
}
@Article{antolik_fncom,
Title = {{Development of maps of simple and complex cells in the primary visual cortex}},
Author = {Antolik, Jan and Bednar, James A},
Journal = {Frontiers in Computational Neuroscience},
Year = {2011},
Number = {17},
Volume = {5},
Doi = {10.3389/fncom.2011.00017},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/antolik_fncom11.pdf:PDF},
Url = {http://www.frontiersin.org/computational_neuroscience/10.3389/fncom.2011.00017/abstract}
}
@Article{bednar_jpp12,
Title = {{Building a mechanistic model of the development and function of the primary visual cortex}},
Author = {Bednar, James A.},
Journal = {Journal of Physiology-Paris},
Year = {2012},
Month = {September},
Number = {5-6},
Pages = {194--211},
Volume = {106},
Doi = {10.1016/j.jphysparis.2011.12.001},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/bednar_jpp12.pdf:PDF},
ISSN = {0928-4257},
Url = {http://dx.doi.org/10.1016/j.jphysparis.2011.12.001}
}
@Article{bednar_bmm08,
Title = {{Understanding Neural Maps with Topographica}},
Author = {James A. Bednar},
Journal = {Brains, Minds, and Media},
Year = {2008},
Pages = {bmm1402},
Volume = {3},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/bednar_bmm08.pdf:PDF}
}
@Book{bednar_fnc16,
Title = {{Neural Maps: Their Function and Development}},
Author = {James A. Bednar and Christopher K. I. Williams},
Publisher = {MIT Press},
Year = {2016},
Note = {In press.},
Series = {Computational Neuroscience},
Volume = {From Neuron to Cognition},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/bednar_fnc16.pdf:PDF}
}
@Article{blasdel_nature86,
Title = {{Voltage-sensitive dyes reveal a modular organization in monkey striate cortex.}},
Author = {Blasdel, Gary and Salama, Guy},
Journal = {Nature},
Year = {1986},
Number = {6070},
Pages = {579--585},
Volume = {321},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/blasdel_nature86.pdf:PDF},
Url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=abstract&list_uids=3713842}
}
@Article{blasdel_jn92a,
Title = {{Differential imaging of ocular dominance and orientation selectivity in monkey striate cortex}},
Author = {Gary G. Blasdel},
Journal = {The Journal of Neuroscience},
Year = {1992},
Number = {8},
Pages = {3115-3138},
Volume = {12},
Eprint = {http://www.jneurosci.org/content/12/8/3115.full.pdf+html},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/blasdel_jn92a.pdf:PDF},
Url = {http://www.jneurosci.org/content/12/8/3115.abstract}
}
@Article{blasdel_jn92b,
Title = {{Orientation Selectivity, Preference, and Continuity in Monkey Striate Cortex}},
Author = {Gary G. Blasdel},
Journal = {The Journal of Neuroscience},
Year = {1992},
Pages = {3139--3161},
Volume = {12},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/blasdel_jn92b.pdf:PDF},
Url = {http://www.jneurosci.org/cgi/content/abstract/12/8/3139}
}
@Manual{bokeh_manual,
Title = {{Bokeh: Python library for interactive visualization}},
Author = {{Bokeh Development Team}},
Year = {2014},
Url = {http://www.bokeh.pydata.org}
}
@Article{romain_jcn07,
Title = {{Simulation of networks of spiking neurons: A review of tools and strategies}},
Author = {Romain Brette and 21 others},
Journal = {Journal of Computational Neuroscience},
Year = {2007},
Month = {December},
Pages = {349--398},
Volume = {23},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/romain_jcn07.pdf:PDF},
Model_link = {http://senselab.med.yale.edu/senselab/ModelDB/ShowModel.asp?model=83319},
Preprint = {http://arxiv.org/abs/q-bio/0611089v2}
}
@Article{bringuier_science99,
Title = {{Horizontal Propagation of Visual Activity in the Synaptic Integration Field of Area 17 Neurons}},
Author = {Vincent Bringuier and Fr\'{e}d\'{e}ric Chavane and Larry Glaeser and Yves Fr/'{e}gnac},
Journal = {Science},
Year = {1999},
Month = {January},
Pages = {695--699},
Volume = {283},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/bringuier_science99.pdf:PDF}
}
@Article{brown_frontiers14,
Title = {{The tale of the neuroscientists and the computer: why mechanistic theory matters}},
Author = {Brown, Joshua W.},
Journal = {Frontiers in Neuroscience},
Year = {2014},
Number = {349},
Volume = {8},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/brown_frontiers02.pdf:PDF},
ISSN = {1662-453X}
}
@Article{buzas_compneurol02,
Title = {{Axonal topography of cortical basket cells in relation to orientation, direction, and ocular dominance maps}},
Author = {Buz\'{a}s, P\'{e}ter and Eysel, Ulf T. and Adorj\'{a}n, P\'{e}ter and Kisv\'{a}rday, Zol\'{a}n F.},
Journal = {The Journal of Comparative Neurology},
Year = {2001},
Number = {3},
Pages = {259--258},
Volume = {437},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/buzas_jcompneurol01.pdf:PDF}
}
@Article{buzas_compneurol06,
Title = {{Model-Based Analysis of Excitatory Lateral Connections in the Visual Cortex}},
Author = {Buz\'{a}s, P\'{e}ter and Kov\'{a}cs, Krisztina and Ferecsk\'{o}, Alex S. and Budd, Julian M. L. and Eysel, Ulf T. and Kisv\'{a}rday, Zolt\'{a}n F.},
Journal = {The Journal of Comparative Neurology},
Year = {2006},
Number = {6},
Pages = {861--881},
Volume = {499},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/buzas_compneurol06.pdf:PDF}
}
@Article{carandini_nature12,
Title = {{Normalization as a canonical neural computation}},
Author = {Matteo Carandini and David J. Heeger},
Journal = {Nature Reviews Neuroscience},
Year = {2012},
Month = {January},
Pages = {51--62},
Volume = {13},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/carandini_nature12.pdf:PDF}
}
@Article{chapman_jn96,
Title = {{Development of orientation preference maps in ferret primary visual cortex}},
Author = {Chapman, B and Stryker, M P and Bonhoeffer, T},
Journal = {The Journal of Neuroscience},
Year = {1996},
Month = {October},
Number = {20},
Pages = {6443--6453},
Volume = {16},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/chapman_jn96.pdf:PDF}
}
@Article{chemla_jphys10,
Title = {{Voltage-sensitive dye imaging: Technique review and models}},
Author = {Chemla, S. and Chavane, F.},
Journal = {Journal of Physiology-Paris},
Year = {2010},
Month = {January},
Number = {1-2},
Pages = {40--50},
Volume = {104},
Abstract = {{In this review, we present the voltage-sensitive dye imaging (VSDI) method. The possibility offered for in vivo (and in vitro) brain imaging is unprecedented in terms of spatial and temporal resolution. However, the unresolved multi-component origin of the optical signal encourages us to perform a detailed analysis of the method limitation and the existing models. We propose a biophysical model at a mesoscopic scale in order to understand and interpret this signal.}},
Day = {10},
Doi = {10.1016/j.jphysparis.2009.11.009},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/chemla_jpp10.pdf:PDF},
ISSN = {09284257},
Url = {http://dx.doi.org/10.1016/j.jphysparis.2009.11.009}
}
@Article{chemla_neuroimage10,
Title = {{A biophysical cortical column model to study the multi-component origin of the VSDI signal}},
Author = {S. Chemla and F. Chavane},
Journal = {NeuroImage},
Year = {2010},
Number = {2},
Pages = {420 - 438},
Volume = {53},
Doi = {DOI: 10.1016/j.neuroimage.2010.06.026},
File = {:Users/jstevens/Desktop/material/papers/pdfs/chemla_neuroimage10.pdf:PDF},
ISSN = {1053-8119},
Url = {http://www.sciencedirect.com/science/article/pii/S1053811910008700}
}
@Article{coppola_pnas98,
Title = {{Unequal Representation of Cardinal and Oblique Contours in Ferret Visual Cortex}},
Author = {D. M. Coppola and L. E. White and D. Fitzpatrick and D. Purves},
Journal = {Proceedings of the National Academy of Sciences},
Year = {1998},
Number = {5},
Pages = {2621--2623},
Volume = {95},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/coppola_pnas98.pdf:PDF}
}
@Article{crair_science98,
Title = {{The Role of Visual Experience in the Development of Columns in Cat Visual Cortex}},
Author = {Crair, Michael C. and Gillespie, Deda C. and Stryker, Michael P},
Journal = {Science},
Year = {1998},
Month = {January},
Number = {5350},
Pages = {566--570},
Volume = {279},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/crair_science98.pdf:PDF}
}
@Article{crick_arxiv15,
Title = {{Dear CAV, We Need to Talk About Reproducibility}},
Author = {Tom Crick and Benjamin A. Hall and Samin Ishtiaq},
Journal = {arXiv},
Year = {2015},
Pages = {1-9},
Volume = {abs/1502.02448},
File = {:Users/jstevens/Desktop/material/papers/pdfs/crick_arxiv15.pdf:PDF},
Keywords = {reproducibility}
}
@Article{deangelis_tin95,
Title = {{Receptive-field dynamics in the central visual pathways}},
Author = {Gregory C. DeAngelis and Izumi Ohzawa and Ralph D. Freeman},
Journal = {Trends in Neurosciences },
Year = {1995},
Number = {10},
Pages = {451 - 458},
Volume = {18},
Doi = {http://dx.doi.org/10.1016/0166-2236(95)94496-R},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/deangelis_tins95.pdf:PDF},
ISSN = {0166-2236}
}
@Conference{drummond_icml09,
Title = {{Replicability in not Reproducibility: Nor is it Good Science}},
Author = {Drummond, Chris},
Booktitle = {The 4th workshop on Evaluation Methods for Machine Learning},
Year = {2009},
Address = {Montreal, Canada},
Month = {June},
File = {:Users/jstevens/Desktop/material/papers/pdfs/drummond_icml09.pdf:PDF},
Url = {http://www.site.uottawa.ca/ICML09WS/papers/w2.pdf}
}
@InProceedings{elver_hpca14,
Title = {{TSO-CC: Consistency directed cache coherence for TSO}},
Author = {Marco Elver and Vijay Nagarajan},
Booktitle = {HPCA},
Year = {2014},
Pages = {165-176},
Website = {http://homepages.inf.ed.ac.uk/s0787712/research/tsocc}
}
@Article{erwin_nc95,
Title = {{Models of orientation and ocular dominance columns in the visual cortex: a critical comparison}},
Author = {Erwin, E and Obermayer, K and Schulten, K},
Journal = {Neural Computation},
Year = {1995},
Month = {May},
Number = {3},
Pages = {425--468},
Volume = {7},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/erwin_nc95.pdf:PDF}
}
@Article{gallant_neuroreport98,
Title = {{Neural activity in areas V1, V2 and V4 during free viewing of natural scenes compared to controlled viewing}},
Author = {Jack L. Gallant and Charles E. Connor and David C. Van Essen},
Journal = {Neuroreport},
Year = {1998},
Month = {January},
Number = {1},
Pages = {2153--2158},
Volume = {9},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/gallant_neuroreport98.pdf:PDF}
}
@Article{gent_corr13,
Title = {{The Recomputation Manifesto}},
Author = {Ian P. Gent},
Journal = {Computing Reasearch Repository},
Year = {2013},
Pages = {1-6},
Volume = {abs/1304.3674},
File = {:Users/jstevens/Desktop/material/papers/pdfs/gent_corr13.pdf:PDF},
Url = {http://arxiv.org/abs/1304.3674}
}
@Article{grinvald_natneuro05,
Title = {{VSDI: a new era in functional imaging of cortical dynamics}},
Author = {Grinvald, Amiram and Hildesheim, Rina},
Journal = {Nature Reviews Neuroscience},
Year = {2004},
Month = {November},
Number = {11},
Pages = {874--885},
Volume = {5},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/grinvald_natneuro05.pdf:PDF}
}
@Article{gur_cerebral05,
Title = {{Orientation and Direction Selectivity of Neurons in V1 of Alert Monkeys: Functional Relationships and Laminar Distributions}},
Author = {Gur, Moshe and Kagan, Igor and Snodderly, D. Max},
Journal = {Cerebral Cortex},
Year = {2005},
Number = {8},
Pages = {1207--1221},
Volume = {15},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/gur_cerebral05.pdf:PDF}
}
@Book{hebb_book49,
Title = {{The Organization of Behavior}},
Author = {Hebb, Donald O.},
Publisher = {John Wiley},
Year = {1949},
Address = {New York},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/hebb_book49.pdf:PDF}
}
@Article{hubel_jphysio59,
Title = {{Receptive fields of single neurones in the cat's striate cortex}},
Author = {Hubel, D. H. and Wiesel, T. N.},
Journal = {The Journal of Physiology},
Year = {1959},
Month = {October},
Number = {3},
Pages = {574--591},
Volume = {148},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/hubel_jphysio59.pdf:PDF}
}
@Article{hunter_ieee07,
Title = {{Matplotlib: A 2D graphics environment}},
Author = {Hunter, J. D.},
Journal = {Computing In Science \& Engineering},
Year = {2007},
Number = {3},
Pages = {90--95},
Volume = {9},
Abstract = {Matplotlib is a 2D graphics package used for Python
for application development, interactive scripting, and
publication-quality image generation across user
interfaces and operating systems.},
File = {:/Users/jstevens/Desktop/material/papers/pdfs/hunter_ieee07.pdf:PDF},
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