isotools

command-line tools for calculating cluster quality.

Summary

The software is intended for use with clusters formed from of feature vectors of neural extracellular field recordings.

These programs were tested/developed on LINUX systems, but can be compiled to run on Microsoft Windows or Mac OS. To compile, you will need a standard C++ compiler and the make utility. Compile the C++ files from the command line with the make command. That will produce executable files. The intermediate .o files can be removed with make clean. make install will copy the binary files to the top-level directory (isoitools).

Contains

src - source code directory, along with documentation in readme files in subdirectories

src/isoi - source code for program that calculates Isolation Information cluster quality measures

src/isorat - source code for program that calculates Isolation Distance and LRatio cluster quality measures

src/wave2f - source code for program that

wavex.txt - short recording of extracellular waveforms using a tetrode in rat CA1. The format of the file allows using it with wave2f. The first line of the file is the number of microwires used for recording (4, since a tetrode). The next line is the number of samples on each channel (64). The following line specifies the sampling frequency (32 KHZ). The remaining lines are the waveform data for each spike (4 channels at 64 samples per channel, so 256 numbers per line).

Installation

To build the software, change to the src directory and use the make command. Then run the make install command. This will copy the binaries for the 3 programs above into the top-level directory. The usage instructions and further information on each of the programs is located in the subdirectories as readme.txt files.

Use

wavex.txt is a sample data file that can be used with these programs.

The following instructions demonstrate how to use the programs:

1. use wave2f to convert the waveforms into feature vectors & save results to file: wave2f wavex.txt wavefeat.txt
2. use isoi to obtain the Isolation Information quality measures & save results to file: isoi wavefeat.txt wave_IsoI.txt
3. use isorat to obtain the Isolation Distance and LRatio quality measures & save results to file: isorat wavefeat.txt wave_IsoDLRat.txt

Please consult the individual readme.txt files for more information on the individual programs (located in the src subdirectories).

Contact

For more information contact Sam Neymotin ( samn at neurosim dot downstate dot edu ) or Andre Fenton ( afenton at nyu dot edu ).

References

The methods used in these program are described in an article in press at The Journal of Neuroscience,

Measuring the quality of neuronal identification in ensemble recordings
by Neymotin SA, Lytton WW, Olypher AO, Fenton AA (2011).

License

Copyright (C) 2003-2011 Sam Neymotin & BioSignal Group

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/. </license info>