Measuring neuronal identification quality in ensemble recordings (isoitools) (Neymotin et al. 2011)

 Download zip file 
Help downloading and running models
Accession:141061
"... Here we describe information theoretic measures of action potential waveform isolation applicable to any dataset, that have an intuitive, universal interpretation, and that are not dependent on the methods or choice of parameters for single unit isolation, and that have been validated using a dataset."
Reference:
1 . Neymotin SA, Lytton WW, Olypher AO, Fenton AA (2011) Measuring the quality of neuronal identification in ensemble recordings Journal of Neuroscience 31(45):16398-16409 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type:
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program;
Model Concept(s): Action Potentials; Methods; Extracellular Fields;
Implementer(s): Neymotin, Sam [samn at neurosim.downstate.edu];
  
/
isoitools
src
readme.txt
wavex.txt
                            
isoitools - command-line tools for calculating cluster quality.
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).

layout of files:

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

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

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

    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).

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.

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).

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 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 info>
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>