Spike Train Toolkit
     - Primer
     - Introduction
     - Toolkit Wiki
     - Download
     - Demonstrations
     - Input Format
     - Input Structures
     - Output Structures
     - Information Options
     - Entropy Options
     - Function Reference
     - Version History
     - License
     - Contribute
  Analysis Overview
     - Analyze Data
     - Your Submissions
  BrainML Models
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User ID

  Computational Neuroinformatics Tools for Analysis of Spike Train Data

Feb 12, 2010 News

We are proud to announce a new release of the STAToolkit, version 1.5! The STAToolkit now works with Octave (version 3.0.1 or greater). Please see the detailed Version History for more information. To download the new release please go to the Download page.

Jan 29, 2010 News

We are proud to announce a new release of the STAToolkit, version 1.4! This version augments the input data format and input data structures to allow for reading (staread) and writing (stawrite) continuous data (e.g., LFP). Function binless is now able to handle continuous data; see the new demo. Please see the detailed Version History for more information. To download the new release please go to the Download page.

Jan 20, 2010 News

We are proud to announce a new release of the STAToolkit, version 1.3! This version includes a new information method, the context-tree weighting Markov chain Monte Carlo algorithm (CTWMCMC). For more information, please see the Introduction page, and the detailed Version History. To download the new release please go to the Download page.

Dec 29, 2009 News

To better guide users of STAToolkit and neuroanalysis.org, we have we have added new tutorial and informative material, including:
  • a new Primer: What will the Spike Train Analysis Toolkit tell me about my data?,
  • a new fast-track Getting Started section to the Introduction that concisely summarize how a neurophysiologist user can use the kind and amount of data recorded by his or her protocols to select appropriate STAToolkit methods, and
  • a newly-expanded Spike Train Analysis Toolkit Demonstrations page that now includes a tutorial on using our demo scripts to evaluate which methods best suit each user's data.
At the 2010 Biophysical Society Annual Meeting, our poster entitled Neuroanalysis.org: Information- Theoretic and Extended Analyses of Neural Coding, by Michael A. Repucci, David H. Goldberg, Eliza Chan, Ajit Jagdale, Jonathan D. Victor, Daniel Gardner, will be presented on board B609 in the Neuronal Systems & Modeling session on Sunday, 21 February 2010.

Nov 3, 2009 News

We have added two buttons to this site's homepage to encourage feedback from our users. The first links to a questionnaire intended for STAToolkit users to learn how they have used the toolkit. The second button links to a questionnaire soliciting ideas from current and future users about what direction better helps their research efforts.

Oct 7, 2009 News

At the SfN Annual Meeting, we offer two neuroanalysis.org and STAToolkit related events:
  • The STAToolkit will be one of Neuroinformatics' Greatest Hits presented at this year's Neuroinformatics Special Interest Social on Sunday, Oct 18, from 6:45 PM - 8:45 PM in McCormick Center Room N140.
  • Our poster detailing new and planned capabilities for neuroanalysis.org: Expansion and integration of neurodatabase.org and neuroanalysis.org toward enhanced data discovery and analysis by D. Gardner, E. Chan, D. H. Goldberg, A. Jagdale, M. A. Repucci, and J. D. Victor will be presented in the Methods for Extracellular Spike Train Analysis session Wednesday morning, Oct 21, as poster 789.10 on board HH2.
This project complements our development at neurodatabase.org of searchable neurophysiology databases containing spike train and other microelectrode data and allied descriptive metadata including recording site, technique, and stimulus. To aid data sharing and interoperability among neurodatabases, we have also created BrainML, an XML-based multilevel data description suite for neuroscience.

Our work in computational neuroinformatics is a component of the Human Brain Project, supported by the NIH and NSF via NIMH. To advance our understanding of neural coding, we have developed the STAToolkit, a suite of information-theoretic algorithms as a public resource for Open Source download. We are extending the capabilities of the STAToolkit with additional information-theoretic tools, as well as additional measures for synchrony, variability, and dimensional reduction to aid tractability of multineuron analyses.

To assist neurophysiologists in applying STAToolkit algorithms for computationally-intensive explorations of databased spike trains, we also offer the AnalysisServer, an open-access dedicated large-scale computational array. To schedule an analysis job for processing, please use the links above or to the left, or contact us at neurodatabase (AT) med.cornell.edu.

User feedback is essential to enhance the power and ease of use of our resources. Should you wish to be added to our growing user list for the STAT Toolkit, please email us at neurodatabase (AT) med.cornell.edu. We are also creating a wiki and additional tutorials for the downloadable STAToolkit and the AnalysisServer.

Funded by Human Brain Project/Neuroinformatics via MH68012 from NIMH, NINDS, NIA, NIBIB and NSF.

More information on this project can be found at the Spike Train Analysis Toolkit home page.


Weill Medical College of Cornell University