The INSTANT Neuronal Spike-Train ANalysis Toolbox

Martin Nilsson, RISE Research Institutes of Sweden (E-mail: [email protected])

Introduction

The INSTANT Neuronal Spike-Train ANalysis Toolbox is a program that inputs a spike train and estimates the corresponding neuronal parameters. This program also estimates errors and performs statistical tests of stationarity and independence. The program is implemented in MATLAB.

The INSTANT software and data is part of the supplemental material for the article Nilsson and Jörntell (2021): "Channel current fluctuations conclusively explain neuronal encoding of internal potential into spike trains", DOI: 10.1103/physreve.103.022407.

Manual

A user manual for INSTANT in PDF format is available as instant-manual.pdf.

Code and installation

The source code is available as the ZIP archive instant.zip or alternatively, as the Base64-encoded ZIP-archive instant.txt. This file can be decoded under the Microsoft Windows operating systems using the command

certutil -decode instant.txt instant.zip

The source code can be loaded into MATLAB and executed. This requires a MATLAB license. INSTANT was developed using version 2013a of MATLAB. The compatibility with later versions is not guaranteed.

Compiled code is available as instant.exe. This can be executed without any MATLAB license by first downloading and installing the MATLAB Compiler Runtime (MCR) version 2013a (8.1), 32-bit. To find the MCR, go to the MathWorks web site and search for "runtime". The URL looks like:

https://se.mathworks.com/products/compiler/matlab-runtime.html

The MCR file is named

MCR_R2013a_win32_installer.exe

Follow the installation instructions on the web page.

After installing the MCR, you can start INSTANT by double clicking instant.exe. Beware that there is sometimes an error on first startup. This is usually resolved by starting a second time.

Spike train data input format and sample files

Input data for INSTANT are text files having one value on each line. This value can be either the length of an interspike interval (ISI) or the time when a spike occurred. INSTANT will automatically determine the type of file. The default time unit is milliseconds. A scale factor can be given in INSTANT.

For testing purposes, there is a file of synthetic spike train data, synthetic-spike-train.txt.

Metadata are saved as .mat-files and can be loaded independently into INSTANT.

Fourteen recorded sample spike trains are available separately at DOI 10.1103/physreve.103.022407 (click "Supplementary Material"). Metadata is also available in the same location.

Processed data output sample files

The output from INSTANT for all sample spike trains are collected in the file instant-combined-output.pdf. In addition, computed parameters are summarized in the file parameter-data.xls.

For more information

Please see the manual instant-manual.pdf for details.