References and links

References in related scientific subject areas:

SIM: Substrate-independent Minds

Foundations: Pattern survival versus Gene survival (Randal A. Koene)

Foundations: Substrate-Independent Minds (Randal A. Koene)

Foundations: A Window of Opportunity (Randal A. Koene)

Substrate-Independence: A thread about terminology, definitions and subsets

2045: Global Future 2045: Towards a New Strategy for Human Evolution, Congress Proceedings

2045: 2045.com & Global Future 2045

Carboncopies: Permalinks page to Recent and Interesting Discussions on the carboncopies Facebook group

Keith Wiley and Randal A. Koene (2015). The Fallacy of Favoring Gradual Replacement Mind Uploading Over Scan-and-Copy. (Preprint). Also available as PDF.

Keith Wiley (2014). A Taxonomy and Metaphysics of Mind-Uploading. Humanity+ Press and Alautun Press.

Blackford, R. and Broderick, D. (Eds.) (2014). Intelligence Unbound: The Future of Uploaded and Machine Minds, Wiley-Blackwell, Oxford, UK, pre-print of contributed chapter by Koene, R.A.: Feasible Mind Uploading, original title: System Identification: The foundation of modern science and the core of feasible mind uploading

SIM: Whole Brain Emulation

Koene, R.A and Deca, D. (Eds.) (2013). Brain Emulation and Connectomics: a Convergence of Neuroscience and Artificial General Intelligence, Special Issue of the Journal of Artificial General Intelligence, Vol.4, No.3, doi:10.2478/jagi-2013-0005 to doi:10.2478/jagi-2013-0012: http://www.carboncopies.org/call-for-papers-jagi-special-issue-on-brain-emulation-and-connectomics-a-convergence-of-neuroscience-and-artificial-general-intelligence

Koene, R.A. (2012). Fundamentals of Whole Brain Emulation: State, Transition and Update Representations, Special Issue of the International Journal on Machine Consciousness, Vol.4, No.1, (pre-print): http://www.carboncopies.org/research-projects/articles-and-essays/koene.IJMC.fundamentals-of-WBE-state-transition-and-update-representations.proofs-20120410.pdf

Koene, R.A. (2012). Experimental Research in Whole Brain Emulation: The Need for Innovative In-Vivo Measurement Techniques, Special Issue of the International Journal on Machine Consciousness, Vol.4, No.1, (pre-print): http://www.carboncopies.org/research-projects/articles-and-essays/koene.IJMC.experimental-research-in-WBE-the-need-for-innovative-in-vivo-measurement-techniques.proofs-20120410.pdf

Whole Brain Emulation: Roadmap (v1.0, 2007-2008, Future of Humanity Institute)

The Society of Neural Prosthetics and Whole Brain Emulation Science: minduploading.org

The Neural Prostheses Foundation investigating Transfer of Functions of the Mind: NeuralProstheses.Org

Whole Brain Emulation and the Nematode (Jeff Kaufman)

National Acadamy of Engineering's 14 "Grand Challenges for Engineering": Reverse-engineer the brain

Lee, Wei-Chung Allen and Bonin, Vincent and Reed, Michael and Graham, Brett J. and Hood, Greg and Glattfelder, Katie and Reid, R. Clay. (2016). Anatomy and function of an excitatory network in the visual cortex, Nature, doi: 10.1038/nature17192: http://dx.doi.org/10.1038/nature17192, http://nature.com/articles/doi:10.1038/nature17192 (nature.com content sharing initiative online access to full article)

Neuroscience: Large-Scale High-Resolution Brain Simulation and Neuroinformatics

Tim Dettmers. (2015). The Brain vs Deep Learning Part I: Computational Complexity — Or Why the Singularity Is Nowhere Near: https://timdettmers.wordpress.com/2015/07/27/brain-vs-deep-learning-singularity/

Neurokernel: An open source platform for emulating the fruit fly brain: http://neurokernel.github.io/ (Aurel Lazar)

Kozloski, J. and Wagner, J. (2011). An Ultrascalable Solution to Large-scale Neural Tissue Simulation, Frontiers in Neuroinformatics, Vol. 5, No.15, doi: 10.3389/fninf.2011.00015: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3175572/

Parker, A.C., Friesz, A.K., and Pakdaman, A. (2006). Towards a Nanoscale Artificial Cortex, presented at The 2006 International Conference on Computing in Nanotechnology (CNAN'06), June 26-29, 2006, Las Vegas, USA: http://eve.usc.edu/Publications/NanoscaleArtificialCortex.pdf

BlueBrain project: http://bluebrain.epfl.ch/ (Henry Markram)

NeuroModeling Geometric Reconstruction project: http://cvcweb.ices.utexas.edu/cvcwp/?page_id=176 (Computational Visualization Center, Institute for Computational Engineering and Sciences, University of Texas at Austin)

Multi-Scale Object Oriented Simulation Environment (MOOSE): http://moose.sourceforge.net/ (Upinder S. Bhalla)

R. Appali, U. van Rienen and T. Heimburg. (2012). A comparison of the Hodgkin-Huxley model and the soliton theory for the action potential in nerves. Advances in Planar Lipid Bilayers and Liposomes 16: 275-299: http://www.membranes.nbi.dk/pdf/2012_AppalivanRienenHeimburg_APLBL.pdf

Neuroscience: Large-Scale High-Resolution Brain Data Acquisition and Connectomics

Shawn Mikula. (2016). Progress Towards Mammalian Whole-Brain Cellular Connectomics, Frontiers in Neuroanatomy, http://dx.doi.org/10.3389/fnana.2016.00062: http://journal.frontiersin.org/article/10.3389/fnana.2016.00062/full

Robert L. McIntyre and Gregory M. Fahy. (2015). Aldehyde-stabilized cryopreservation, Cryobiology, doi: http://dx.doi.org/10.1016/j.cryobiol.2015.09.003: http://www.sciencedirect.com/science/article/pii/S001122401500245X

Samuel G. Rodriques, Adam H. Marblestone, Max Mankin, Lowell Wood, Edward

Boyden. (2013). Multiplexed Neural Recording Down a Single Optical Fiber via

Optical Reflectometry with Capacitive Signal Enhancement, arXiv:1506.01033: http://arxiv.org/abs/1506.01033

Narayanan Kasthuri, Kenneth Jeffrey Hayworth, Daniel Raimund Berger, Richard Lee Schalek, José Angel Conchello, Seymour Knowles-Barley, Dongil Lee, Amelio Vázquez-Reina, Verena Kaynig, Thouis Raymond Jones, Mike Roberts, Josh Lyskowski Morgan, Juan Carlos Tapia, H. Sebastian Seung, William Gray Roncal, Joshua Tzvi Vogelstein, Randal Burns, Daniel Lewis Sussman, Carey Eldin Priebe, Hanspeter Pfister, Jeff William Lichtman. (2015). Saturated Reconstruction of a Volume of Neocortex, Cell, Volume 162, Issue 3, p648–661, 30 July 2015. DOI: http://dx.doi.org/10.1016/j.cell.2015.06.054

And the press release: http://www.eurekalert.org/pub_releases/2015-07/cp-tat072815.php

With video: https://www.youtube.com/watch?t=16&v=nEOpUypJgyw

Marblestone, A.H., Bradley M. Zamft, Yael G. Maguire, Mikhail G. Shapiro, Thaddeus R. Cybulski, Joshua I. Glaser, Ben Stranges, Reza Kalhor, David A. Dalrymple, Dongjin Seo, Elad Alon, Michel M. Maharbiz, Jose Carmena, Jan Rabaey, Edward S. Boyden, George M. Church, Konrad P. Kording. (2013). Physical Principles for Scalable Neural Recording, Frontiers in Computational Neuroscience, 7:137. doi: 10.3389/fncom.2013.00137; http://journal.frontiersin.org/Journal/10.3389/fncom.2013.00137/abstract;

And the arXiv version, arXiv:1306.5709v1: http://arxiv.org/abs/1306.5709

Adam H Marblestone, Evan R Daugharthy, Reza Kalhor, Ian Peikon, Justus Kebschull, Seth L Shipman, Yuriy Mishchenko, David A Dalrymple, Bradley M Zamft, Konrad P Kording, Edward S Boyden, Anthony M Zador, George M Church. (2013). Conneconomics: The Economics of Large-Scale Neural Connectomics, bioRxiv, doi: 10.1101/001214: http://biorxiv.org/content/early/2013/12/16/001214

Adam H Marblestone, Evan R Daugharthy, Reza Kalhor, Ian D Peikon, Justus M Kebschull, Seth L Shipman, Yuriy Mishchenko, Je Hyuk Lee, Konrad P Kording, Edward S Boyden, Anthony M Zador, George M Church. (2014). Rosetta Brains: A Strategy for Molecularly-Annotated Connectomics, arXiv:1404.5103 [q-bio.NC]: http://arxiv.org/abs/1404.5103

Thaddeus R. Cybulski, Joshua I. Glaser, Adam H. Marblestone, Bradley M. Zamft, Edward S. Boyden, George M. Church, Konrad P. Kording. (2014). Spatial Information in Large-Scale Neural Recordings, arXiv:1402.3375 [q-bio.NC]: http://arxiv.org/abs/1402.3375

Dongjin Seo, Jose M. Carmena, Jan M. Rabaey, Elad Alon, Michel M. Maharbiz. (2013). Neural Dust: An Ultrasonic, Low Power Solution for Chronic Brain-Machine Interfaces, arXiv:1307.2196 [q-bio.NC]: http://arxiv.org/abs/1307.2196

Daniel R Hochbaum, Yongxin Zhao, Samouil L Farhi, Nathan Klapoetke, Christopher A Werley, Vikrant Kapoor, Peng Zou, Joel M Kralj, Dougal Maclaurin, Niklas Smedemark-Margulies, Jessica L Saulnier, Gabriella L Boulting, Christoph Straub, Yong Ku Cho, Michael Melkonian, Gane Ka-Shu Wong, D Jed Harrison, Venkatesh N Murthy, Bernardo L Sabatini, Edward S Boyden, Robert E Campbell & Adam E Cohen. (2014). All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins, Nature Methods, doi:10.1038/nmeth.3000: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3000.html?message-global=remove

R. Prevedel, Y.-G. Yoon, M. Hoffmann, N. Pak, G. Wetzstein, S. Kato, T. Schrödel, R. Raskar, M. Zimmer, E.S. Boyden, A. Vaziri. (2014). Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy, Nature Methods, doi:10.1038/nmeth.2964: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2964.html

Preprint: arXiv:1401.5333: http://arxiv.org/abs/1401.5333

James Kunert, Eli Shlizerman, J. Nathan Kutz. (2014). Low-dimensional functionality of complex network dynamics: Neurosensory integration in the Caenorhabditis elegans connectome, Physical Review E, 89, 052805, DOI: http://dx.doi.org/10.1103/PhysRevE.89.052805

Preprint: arXiv:1310.6689: http://arxiv.org/abs/1310.6689

Briggman, K.L., Helmstaedter, M., and Denk, W. (2011). Wiring Specificity in the Direction-Selectivity circuit of the retina, Nature, Vol.471, 183-188: http://www.nature.com/nature/journal/v471/n7337/full/nature09818.html

Bock, D.D., Lee, W.-C.A., Kerlin, A.M., Andermann, M.L., Hood, G., Wetzel, A.W., Yurgenson, S., Soucy, E.R., Kim, H.S., and Reid, R.C. (2011). Network anatomy and in vivo physiology of visual cortical neurons, Nature, Vol.471, 177-182: http://www.nature.com/nature/journal/v471/n7337/full/nature09802.html

Andres, B., Koethe, U., Kroeger, T., Helmstaedter, M., Briggman, K.L., Denk, W. and Hamprecht, F.A. (2012).  3D Segmentation of SBFSEM Images of Neuropil by a Graphical Model of Supervoxel Boundaries, Medical Image Analysis, Vol.16(4), 796-805, doi:10.1016/j.media.2011.11.004: http://www.sciencedirect.com/science/article/pii/S1361841511001666 (contact rak@carboncopies.org for a PDF of the full article)

Alivisatos AP1, Andrews AM, Boyden ES, Chun M, Church GM, Deisseroth K, Donoghue JP, Fraser SE, Lippincott-Schwartz J, Looger LL, Masmanidis S, McEuen PL, Nurmikko AV, Park H, Peterka DS, Reid C, Roukes ML, Scherer A, Schnitzer M, Sejnowski TJ, Shepard KL, Tsao D, Turrigiano G, Weiss PS, Xu C, Yuste R, Zhuang X. (2013). Nanotools for neuroscience and brain activity mapping. ACS Nano. Mar 26;7(3):1850-66. doi: 10.1021/nn4012847. Epub 2013 Mar 20: http://www.ncbi.nlm.nih.gov/pubmed/23514423

Alivisatos, A.P., Chun, M., Church, G.M., Greenspan, R.J., Roukes, M.L. and Yuste, R. (2012). The Brain Activity Map Project and the Challenge of Functional Connectomics, Neuron, Vol. 74(6), 970-974. doi:10.1016/j.neuron.2012.06.006: http://www.cell.com/neuron/abstract/S0896-6273(12)00518-1

Eric Jonas and Konrad Kording. (2014). Automatic discovery of cell types and microcircuitry from neural connectomics, arXiv:1407.4137: http://arxiv.org/abs/1407.4137

Kording, K.P. (2011). Of toasters and molecular ticker tapes, PLoS Computational Biology, Vol. 7(12): e1002291. doi:10.1371/journal.pcbi.1002291: http://klab.smpp.northwestern.edu/wiki/images/7/7d/Kording_Toaster_Molecular_Ticket_Tapes_2011.pdf

Stevenson, I.H., Kording, K.P. (2011). How advances in neural recording affect data analysis, Nature Neuroscience, Vol.14(2), 139-142: http://klab.wikidot.com/local--files/ian-stevenson/nn.2731.pdf

Osten, P. and Margrie, T.W. (2013). Mapping Brain Circuitry with a Light Microscope, Nature Methods, Vol.10(6), 515-523, doi:10.1038/NMETH.2477: http://www.nature.com/nmeth/journal/v10/n6/pdf/nmeth.2477.pdf

Varshney LR, Chen BL, Paniagua E, Hall DH, Chklovskii DB. (2011). Structural Properties of the Caenorhabditis elegans Neuronal Network. PLoS Computational Biology, 7(2): e1001066. doi:10.1371/journal.pcbi.1001066: http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1001066

White, J.G., Southgate, E., Thomson, J.N., and Brenner, S., F.R.S. (1986). The Structure of the Nervous System of the Nematode Caenorhabditis Elegans, Phil. Trans. Royal Soc. London. Series B, Biol Scien. Vol.314, Issue 1165, 1-340: http://www.wormatlas.org/ver1/MoW_built0.92/toc.html

Expansion Microscopy: http://expansionmicroscopy.org/ (Boyden lab)

Whole-Brain Ultrastructural Mapping: http://homes.mpimf-heidelberg.mpg.de/~smikula/blockface/ (Shawn Mikula)

Mouse Brain Architecture Project: http://brainarchitecture.org/ (Partha Mitra)

ATLUM: http://cbs.fas.harvard.edu/science/connectome-project/atlum (Ken Hayworth)

Also see: http://www.carboncopies.org/gf2045-2013-proceedings/gf2045-2013-proceedings-hayworth

Brainbow 2.0: https://www.mcb.harvard.edu/mcb/news/news-detail/3677/brainbow-20-lichtman-and-sanes-labs/  (Lichtman and Sanes Lab)

KESM: http://research.cs.tamu.edu/bnl/kesm.html (Yoonsuck Choe, Todd Huffman)

Knife-Edge Scanning Microscope Brain Atlas: http://kesm.cs.tamu.edu/

Human Connectome Project: http://www.humanconnectomeproject.org

Human Brain Project: http://www.humanbrainproject.eu/organisation.html

Open Connectome Project: http://openconnectomeproject.org

Connectomes.org Whole-Brain Circuit Reconstruction project web site: connectomes.org (Shawn Mikula)

Comparison of Brain Projects: http://synapticlink.org/BrainProjectComparison.htm

Synthetic Neurobiology Group: http://syntheticneurobiology.org/ (Ed Boyden)

Whole Brain Catalog: http://www.wholebraincatalog.org (twitter: http://twitter.com/#!/BrainCatalog)

WormAtlas: http://www.wormatlas.org/

OpenWorm: http://openworm.org

WormBase: http://wormbase.org (and mirror site http://wormbase.sanger.ac.uk/)

SFN BrainFacts: http://brainfacts.org

Cracking the Neural Code, Third Annual Aspen Brain Forum (2012), Slides and Audio provided in the "Media" section: http://www.nyas.org/Publications/Ebriefings/Detail.aspx?cid=bd737d49-01a9-49b2-a337-681146892540

The Virtual Brain Project: http://thevirtualbrain.org

Neuroscience: Neural Engineering

Hippocampal Prosthesis:

Theodore Berger lab at USC: http://bme.usc.edu/directory/faculty/core-faculty/theodore-w-berger/

Neural-Prosthesis.com: http://www.neural-prosthesis.com/ (Ted Berger) [link may be outdated]

and the Center for Neural Engineering, Theodore W. Berger Labs at USC: http://cne.usc.edu/

Berger, T. W., Song, D., Chan, R. H. M., Marmarelis, V. Z., LaCoss, J., Wills, J., Hampson, R.E., Deadwyler, S.A., Granacki, J. J. (2012). A Hippocampal Cognitive Prosthesis: Multi-Input, Multi-Output Nonlinear Modeling and VLSI Implementation. Ieee Transactions on Neural Systems and Rehabilitation Engineering, 20(2), 198–211. http://doi.org/10.1109/TNSRE.2012.2189133, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3395724/

Herreros, I. and Giovannucci, A. and Taub, A.H. and Hogri, R. and Magal, A. and Bamford, S. and Pruecki, R. and Verschure, P.F.M.J. (2014). A cerebellar neuroprosthetic system: computational architecture and in vivo test, Frontiers in Bioengineering and Biotechnology, Vol.2:14, doi: doi:10.3389/fbioe.2014.00014: http://www.sim.me.uk/neural/JournalArticles/HerrerosEtAl2014.pdf

David J. Guggenmosa, Meysam Azinc, Scott Barbaya, Jonathan D. Mahnkend, Caleb Dunhama, Pedram Mohsenic, and Randolph J. Nudo. (2013). Restoration of function after brain damage using a neural prosthesis, Proceedings of the National Academy of Sciences, Vol.110, No.52, pp. 21177–21182, doi: 10.1073/pnas.1316885110: http://www.pnas.org/content/110/52/21177.full

BrainGate project: http://www.braingate2.org/ (John Donoghue)

Gómez-Martínez, R., Vázquez, P., Duch, M., Muriano, A., Pinacho, D., Sanvicens, N., Sánchez-Baeza, F., Boya, P., de la Rosa, E. J., Esteve, J., Suárez, T. and Plaza, J. A. (2010), Intracellular Silicon Chips in Living Cells. Small, 6: 499–502. doi: 10.1002/smll.200901041: http://onlinelibrary.wiley.com/doi/10.1002/smll.200901041/abstract

Deca, D. and Koene, R.A. (2014). Experimental enhancement of neurphysiological function, Frontiers in Systems Neuroscience, Vol. 8: 189, doi: 10.3389/fnsys.2014.00189: http://journal.frontiersin.org/Journal/10.3389/fnsys.2014.00189/full

Neural Engineering: Computation, Representation, and Dynamics in Neurobiological Systems

Chris Eliasmith, Charles H. Anderson

(or at Amazon)

Neuroscience: Basics

Nicolas Brunel, Vincent Hakim and Magnus JE Richardson. (2014). Single neuron dynamics and computation, Current Opinion in Neurobiology, April 2014, Pages 149–155: http://www.sciencedirect.com/science/article/pii/S0959438814000130

Koch, C. and Marcus, G. (2014). Cracking the Brain’s Codes: How does the brain speak to itself?, MIT Technology Review, June 17: http://www.technologyreview.com/featuredstory/528131/cracking-the-brains-codes/

Principles of Neural Science

Editors:

Eric R. Kandel,

James H. Schwartz,

Thomas M. Jessell,

Steven A. Siegelbaum,

A. J. Hudspeth

Tutorial on Neural Systems Modeling

Thomas J. Anastasio

Biophysics of Computation: Information Processing in Single Neurons

Christof Koch

Information Theory and the Brain

Roland Baddeley, Peter Hancock, Peter Földiák

(or at Amazon)