/crabsort-FItSNE

plugin for the spike-sorting software crabsort that implements FFT-interpolated t-SNE

Primary LanguageMATLABGNU General Public License v3.0GPL-3.0

crabsort-FItSNE

This is a plugin for crabsort

It implements fast Fourier transform-interpolated t-distributed stochastic neighborhood embedding, a type of dimensionality-reduction algorithm.

For more information, see: https://github.com/KlugerLab/FIt-SNE or the paper by Linderman & Steinerberger at https://arxiv.org/abs/1711.04712

Installation

FIt-SNE requires a separate repository.

macOS & GNU/Linux

  1. Download the repository from: https://github.com/KlugerLab/FIt-SNE or clone using
  $ git clone https://github.com/KlugerLab/FIt-SNE
  1. Add the downloaded folder to your MATLAB path
   >> addpath path/to/FIt-SNE`
   >> savepath
  1. Download FFTW from http://www.fftw.org/ or get it for your operating system/distribution
  2. From the root directory of FIt-SNE, run:
  $ g++ -std=c++11 -O3  src/sptree.cpp src/tsne.cpp src/nbodyfft.cpp  -o bin/fast_tsne -pthread -lfftw3 -lm

Windows

Follow steps 1 and 2 above, then go to https://github.com/KlugerLab/FIt-SNE and download the compiled binary instead.