spike-sorting

Repository of spike-sorting applications and related tools and libraries. (C) 2015 Baccus Lab

matlab

Contains source for Matlab GUI sorting application, and C++ source for some compiled mex-functions used by the sorting application

Compiling c++ soure

Include all the names of the source codes in the list compile_mex.m matlab code:

source_codes = {'AutoCorr.cpp', 'CrossCorr.cpp', 'Polygon.cpp'};

Run the following command in the spike-sorting/matlab folder to compile c++ source codes into mex-functions in the command line:

./installmexfiles

extract (Mac)

Contains source code for C++ application to extract spike and noise snippets from raw data HDF5 files.

Making extract requires armadillo, a C++ linear algebra library. If you have homebrew, you can get armadillo by

$ brew install homebrew/science/armadillo

You will also need the HDF5 libraries, if you don't already have them. You can get these by

$ brew install homebrew/science/hdf5

We also use Qt's cross-platform build system to simplify the build process. You can install this by doing:

$ brew install qt

To install extract,

$ cd /path/to/extract/  
$ qmake  
$ make
$ make install # optional  

extract (Linux)

Install required libraries

$ sudo apt install libhdf5-dev qt5-default
$ sudo apt install cmake libopenblas-dev liblapack-dev libarpack2-dev libsuperlu-dev
(recommended packes by official armadillo webpage)	
$ sudo apt install libarmadillo-dev

To install extract,

$ cd /path/to/extract/
$ qmake
$ make

wiki

See the Wiki for more info