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Spike Train Analysis Toolkit: Enabling Wider Application of Information-Theoretic Techniques to Neurophysiology

David H. Goldberg, Jonathan D. Victor, Esther P. Gardner, Daniel Gardner
2009 Neuroinformatics  
STAToolkit is a software package which implements, documents, and guides application of several information-theoretic spike train analysis techniques, thus minimizing the effort needed to adopt and use  ...  In order to facilitate more widespread adoption of these informative methods by the neuroscience community, we have developed the Spike Train Analysis Toolkit.  ...  We thank the many developers of the information-theoretic and entropy measures we have implemented in the toolkit, and the many users of this software.  ... 
doi:10.1007/s12021-009-9049-y pmid:19475519 pmcid:PMC2818590 fatcat:66l2vjknprgr5bho64aobxyzay

Spike Metrics [chapter]

Jonathan D. Victor, Keith P. Purpura
2010 Analysis of Parallel Spike Trains  
An invited chapter for "Analysis of Parallel Spike Trains" (S. Rotter and S. Grün, eds.)  ...  Since spike trains can be considered to be sequences of stereotyped events, it is natural to focus on ways to quantify differences between event sequences, known as spike-train metrics.  ...  We would like to thank Sebastien Louis for his thorough reading of a draft and his thoughtful and helpful comments.  ... 
doi:10.1007/978-1-4419-5675-0_7 fatcat:7rxf4pzytbfvbhtjcwiu5xky2e

Python for information theoretic analysis of neural data

Robin A. A. Ince
2009 Frontiers in Neuroinformatics  
We explain how and why using Python has allowed us to signifi cantly improve the speed and domain of applicability of the information theoretic algorithms, allowing analysis of data sets characterized  ...  In this article, we describe our work and experiences using Python for information theoretic analysis.  ...  Montemurro for useful discussions on the implementation of entropy methods and for important contributions to the development of the information theoretic algorithms.  ... 
doi:10.3389/neuro.11.004.2009 pmid:19242557 pmcid:PMC2647335 fatcat:sj7nvpmokzbjxcny3lza2koori

Extraction of spatio-temporal primitives of emotional body expressions

Lars Omlor, Martin A. Giese
2007 Neurocomputing  
information theoretic spike train analysis.  ...  We report availability of the analysis tools in the first of two planned formats, a Spike Train Analysis Toolkit, available at http://cortex.med.cornell.edu/toolkit.  ... 
doi:10.1016/j.neucom.2006.10.100 fatcat:esivhljzsbcihdl5qbp756josu

Feature extraction from spike trains with Bayesian binning: 'Latency is where the signal starts'

Dominik Endres, Mike Oram
2009 Journal of Computational Neuroscience  
We employ the posterior distributions for an information theoretic analysis of the neural code comprised of latency and firing rate of neurons in high-level visual area STSa.  ...  The peristimulus time histogram (PSTH) and its more continuous cousin, the spike density function (SDF) are staples in the analytic toolkit of neurophysiologists.  ...  Endres was supported by a Medical Research Council (UK) special training fellowship in bioinformatics G0501319. Both authors would like to thank P. Földiak and J.  ... 
doi:10.1007/s10827-009-0157-3 pmid:19449095 fatcat:uvzccp6gsraepcfzyjzg7zv3ni

28th Annual Computational Neuroscience Meeting: CNS*2019

2019 BMC Neuroscience  
The computer then performed online event detection on the signals and forwarded this information to the robot via Bluetooth connection, accurately preserving the temporal structure of the intervals building  ...  supercritical Hopf bifurcation, that in presence of the theta forcing is excited, giving rise to gamma oscillations super imposed on the theta rhythm, somehow similarly to what previously found in [8].  ...  practical applications of information theory.  ... 
doi:10.1186/s12868-019-0538-0 fatcat:3pt5qvsh45awzbpwhqwbzrg4su

26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3

Adam J. H. Newton, Alexandra H. Seidenstein, Robert A. McDougal, Alberto Pérez-Cervera, Gemma Huguet, Tere M-Seara, Caroline Haimerl, David Angulo-Garcia, Alessandro Torcini, Rosa Cossart, Arnaud Malvache, Kaoutar Skiker (+526 others)
2017 BMC Neuroscience  
This formalism underlines a potential mechanism for efficiently transmitting sparse stimulus information, and further suggests sensory pathways may have evolved to take advantage of the sparsity of visual  ...  We demonstrate that the receptive field structure does indeed facilitate marked improvements in natural stimulus encoding at the price of yielding erroneous information about specific classes of stimuli  ...  P224 Information-theoretic analysis of temporal code-driven stimulation applied to electroreception We complement the analysis of the TCDS protocol with a measure based on information theory: Transitions  ... 
doi:10.1186/s12868-017-0372-1 fatcat:q5x3vgivujgshmtthc6ki4fcfu

26th Annual Computational Neuroscience Meeting (CNS*2017): Part 1

Sue Denham, Panayiota Poirazi, Erik De Schutter, Karl Friston, Ho Ka Chan, Thomas Nowotny, Dongqi Han, Sungho Hong, Sophie Rosay, Tanja Wernle, Alessandro Treves, Sarah Goethals (+90 others)
2017 BMC Neuroscience  
This formalism underlines a potential mechanism for efficiently transmitting sparse stimulus information, and further suggests sensory pathways may have evolved to take advantage of the sparsity of visual  ...  We demonstrate that the receptive field structure does indeed facilitate marked improvements in natural stimulus encoding at the price of yielding erroneous information about specific classes of stimuli  ...  P224 Information-theoretic analysis of temporal code-driven stimulation applied to electroreception We complement the analysis of the TCDS protocol with a measure based on information theory: Transitions  ... 
doi:10.1186/s12868-017-0370-3 fatcat:qq2cmqlotbg7vpqlqmmcql4u5i

CORPORATE CONTRIBUTORS

1988 The Hastings center report  
This technique allows for analysis without choosing an arbitrary or poorly motivated bin size, and is a way to extend the standard information analysis techniques to non-Poisson spike trains.  ...  Direct application of information theoretic approaches has revealed that sensory neurons respond most efficiently to sensory signals with natural statistics, although the exact mechanisms enabling such  ...  It is during the application of the transformation that learning also occurs.  ... 
doi:10.1002/j.1552-146x.1988.tb03932.x fatcat:bkotcyah2ngbfdk4kbx3xnf5v4

25th Annual Computational Neuroscience Meeting: CNS-2016

Tatyana O. Sharpee, Alain Destexhe, Mitsuo Kawato, Vladislav Sekulić, Frances K. Skinner, Daniel K. Wójcik, Chaitanya Chintaluri, Dorottya Cserpán, Zoltán Somogyvári, Jae Kyoung Kim, Zachary P. Kilpatrick, Matthew R. Bennett (+597 others)
2016 BMC Neuroscience  
I will discuss theoretical results that point to functional advantages of splitting neural populations into subtypes, both in feedforward and recurrent networks.  ...  Part of this complexity is related to the number of different cell types that work together to encode stimuli.  ...  The funders had no role in study design, data collection and analysis, the decision to publish, or the preparation of the manuscript.  ... 
doi:10.1186/s12868-016-0283-6 pmid:27534393 pmcid:PMC5001212 fatcat:bt45etzj2bbolfcxlxo7hlv6ju

27th Annual Computational Neuroscience Meeting (CNS*2018): Part One

2018 BMC Neuroscience  
Acknowledgements This work was produced as part of the activities of FAPESP Acknowledgements The research leading to these results has received funding from the Brazilian higher education funding agency  ...  Acknowledgement This project was supported by the GSU Brains and Behavior program Acknowledgements We would like to most importantly thank all our subjects who participated in these studies.  ...  The analysis of these models has included computing mutual information between a stochastic input spike train to the presynaptic synapse, and some sort of representation of the postsynaptic response.  ... 
doi:10.1186/s12868-018-0452-x pmid:30373544 pmcid:PMC6205781 fatcat:xv7pgbp76zbdfksl545xof2vzy

Experimental and Computational Study on Motor Control and Recovery After Stroke: Toward a Constructive Loop Between Experimental and Virtual Embodied Neuroscience

Anna Letizia Allegra Mascaro, Egidio Falotico, Spase Petkoski, Maria Pasquini, Lorenzo Vannucci, Núria Tort-Colet, Emilia Conti, Francesco Resta, Cristina Spalletti, Shravan Tata Ramalingasetty, Axel von Arnim, Emanuele Formento (+11 others)
2020 Frontiers in Systems Neuroscience  
However, since it is technically demanding to model all components of an experiment, traditional approaches to modeling reduce the experimental setups as much as possible.  ...  To this aim, we propose an approach that allows continuous integration of new experimental data into a computational modeling framework.  ...  Bjaalie of the Human Brain Project curation team for expert assistance to share data via the Human Brain Project Neuroinformatics Platform.  ... 
doi:10.3389/fnsys.2020.00031 pmid:32733210 pmcid:PMC7359878 fatcat:dynlxdjmcvc6hjog5yeeqrkkvq

Defense Advanced Research Projects Agency (Darpa) Fiscal Year 2015 Budget Estimates

Department Of Defense Comptroller's Office
2014 Zenodo  
DARPA seeks to improve the analysis of large neural data sets by creating interfaces that will allow researchers to generate new models across multiple scales.  ...  The budget request details the proposed investments $80 million to develop new sets of tools for imaging and analytics of neural and synaptic brain activities that will improve diagnosis and care of wounded  ...  -Enhanced co-clustering and binary analysis techniques to enable the automatic identification of re-used components. A.  ... 
doi:10.5281/zenodo.1215345 fatcat:fjzhmynqjbaafk67q2ckcblj2m

Defense Advanced Research Projects Agency (Darpa) Fiscal Year 2016 Budget Estimates

Department Of Defense Comptroller's Office
2015 Zenodo  
The Defense Advanced Research Projects Agency (DARPA) FY2016 amounted to $2.868 billion in the President's request to support high-risk, high-reward research.  ...  FY 2015 Plans: -Develop new software component reuse capabilities to extend application performance to a wider range of realistic scenarios and enable an expanded concept of operations.  ...  automated program analysis techniques for mathematically validating specified security properties of mobile applications.  ... 
doi:10.5281/zenodo.1215366 fatcat:cqn5tyfixjanzp5x3tgfkpedri

Transösophageales Interventrikuläres Delay bei Vorhofflimmern und Kardialer Resynchronisation

M. Heinke, B. Ismer, H. Kühnert, T. Heinke, G. Dannberg, H. R. Figulla
2013 Biomedical Engineering  
In practical applications, however, the number of electrodes is limited and the placing is subject to constraints.  ...  To facilitate the reconstruction, an MRI-or CT-based model of the body is required, which is represented as a volume conductor.  ...  Our gratitude also extends to the Centre for Promotion of Science, as the organizers of Festival of robotics 2012, without which these experiments wouldn't be possible in this extent.  ... 
doi:10.1515/bmt-2013-4154 pmid:24042832 fatcat:qsbz2z3utva6rery74jfw66pe4
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