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

• A pdf version of the documentation is available from https://github.com/nno/burstiDAtor/releases.
• Sources for the documentation are provided in the doc directory.
• Documentation can be built in pdf or html formats using sphinx-doc (http://sphinx-doc.org/latest/install.html) and the Makefile (Unix-like systems) or make.bat (MS Windows systems) in the doc directory.

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.