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A lightweight discharge analysis program for neural extracellular single unit recordings.

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burstiDAtor

burstiDAtor is a lightweight discharge analysis program for neural extracellular single unit recordings.

Features

  • Compute summary statistics for neural spike recordings (e.g. firing frequency, number of spikes, inter-spike interval, number of burst, burst frequency).
  • Burst detection based on criterion of maximum spike intervals to start and continue a burst (dopamine (DA): 80 and 160 ms, Grace & Bunney (1984); serotonine (5HT): 20 and 20 ms, Hajos et al (2007); reticular thalamic nucleus (RTN): 10 and 10 ms; glutamate (GLU-16): 16 and 16 ms; mPFC glutamate (GLU-45), 45 and 45 ms, Laviolette et al (2005) & Hamati et al., (2020)).
  • Supports wavemark analysis in Spike2 (Cambridge ELectronic Design, Cambridge, UK) input files.
  • Implementations in Matlab and Java.
  • Free/Open Source Software (MIT License).

Requirements

  • The Matlab code requires a working installation of Matlab. Unit test use the xUnit framework
  • The Java code requires a Java VM, version 1.6 or later.

Getting started

  • Matlab: see the example in matlab/examples.

  • Java:

    • Non-programmers: download and run the Java archive (BurstiDAtor.jar) from https://github.com/nno/burstiDAtor/releases.

    • Programmers comfortable with using a Java compiler:

      • make build to build Java .class files.
      • make run to build Java .class files and run burstiDAtor.
      • make jar to build a Java archive (.jar) file.
      • Manually run javac burstiDAtor/*.java in the java directory, then run java burstiDAtor/burstiDAtor.

Documentation

Developers

burstiDAtor is developed by:

  • Nikolaas N. Oosterhof
  • Chris A. Oosterhof

Contribution guidelines

The preferred way to contribute is through github: https://github.com/nno/burstiDAtor

Citation

If you use burstiDAtor for a scientific publication, please cite:

Oosterhof, N.N. & Oosterhof, C.A. (2013), BurstiDAtor: A lightweight discharge analysis program for neural extracellular single unit recordings. https://github.com/nno/burstiDAtor.

BibTeX:

@misc{burstiDAtor,
 title =     "BurstiDAtor: A lightweight discharge analysis program for neural extracellular single unit recordings",
 author = "N.N. Oosterhof and C.A. Oosterhof",
 year = "2013",
 url = "https://github.com/nno/burstiDAtor",
}

License

MIT License; for details, see the COPYING file.

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A lightweight discharge analysis program for neural extracellular single unit recordings.

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