Comparison of Spike Sorting Software

Software	Language	Detection	Feature Extraction	Clustering	Drift	Overlap	Large-scale MEA	Publications	Comments
BinaryPursuitSpikeSorting	MATLAB	binary pursuit	N/A	binary pursuit	No	Yes	No	A model-based spike sorting algorithm for removing correlation artifacts in multi-neuron recordings
bpsort	MATLAB	binary pursuit, raw signal threshold with alignment (initialization)	PCA (initialization)	t-distribution MM (initialization)	Yes	Yes	Yes
CBPSpikesortDemo	MATLAB	continuous basis pursuit	continuous basis pursuit	continuous basis pursuit	No	Yes	Yes?	A unified framework and method for automatic neural spike identification
ClusterLizard	C++	raw signal threshold	wavelets + Lillifors test	Euclidean distance	Yes	No	No	An unsupervised online spike-sorting framework
Combinato	Python	raw signal threshold with alignment	wavelets	superparamagnetic clustering + template matching	Yes	No	No	Reliable analysis of single-unit recordings from the human brain under noisy conditions: tracking neurons over hours	GUI for inspecting clusters
EToS	C++	raw signal threshold	multimodality-weighted PCA, multimodality pick-up algorithm, Graph Laplacian features, PCA	Variational Bayes and EM t-distribution and Gaussian mixture model	No	No	No	Spike sorting of heterogeneous neuron types by multimodality-weighted PCA and explicit robust variational Bayes, Accurate spike sorting for multi-unit recording
FMMSpikeSorter	MATLAB	raw signal threshold	focused mixture model	focused mixture model	Yes?	No	Yes?	Multichannel electrophysiological spike sorting via joint dictionary learning and mixture modeling
gpu_python	Python	N/A	N/A	Generalized Polya urn dependent Dirichlet process MM	Yes	No	No	Dependent dirichlet process spike sorting
KFMM	MATLAB	N/A	N/A	Kalman filter EM GMM	Yes	No	No	Kalman filter mixture model for spike sorting of non-stationary data
KiloSort	MATLAB, CUDA C		Spatiotemporal SVD	Template matching via stochastic batch optimization	No	Yes	Yes	Kilosort: realtime spike-sorting for extracellular electrophysiology with hundreds of channels
MoDT	MATLAB, CUDA C	N/A	PCA	Mixture of drifting t-distributions	Yes	No	No	Model-based spike sorting with a mixture of drifting t-distributions
moksm	MATLAB	N/A	N/A	Mixture of drifting t-distributions	Yes	No	No	EM for a mixture of drifting t-distributions
opass	MATLAB	gamma process model	PCA	gamma process model	Yes	Yes	Yes?	Real-time inference for a gamma process model of neural spiking
OpenElectrophy	Python	raw signal threshold, MTEO	PCA, ICA, wavelets	EM GMM, K-means, mean-shift	No	No	No		GUI for manual clustering and inspecting results
OSort	MATLAB	local energy threshold with alignment	N/A	template matching	Yes	No	No	Online detection and sorting of extracellularly recorded action potentials in human medial temporal lobe recordings, in vivo
pebble	C++, MATLAB	?	PCA	ISO-SPLIT	No	No	No	Unimodal clustering using isotonic regression: ISO-SPLIT
phy (previously klustakwik)	Python	raw signal threshold with alignment	PCA	EM GMM, masked EM GMM	No	No	Yes	Spike sorting for large, dense electrode arrays, High-dimensional cluster analysis with the Masked EM Algorithm	GUI for inspecting sorting results. Large, active community
spikesort	MATLAB	raw signal threshold (height + width)	PCA, factor analysis, sparse PCA, t-SNE	1D GMM, 1D k-means	No	No	No		Claims "99.5% accuracy." Only supports clustering into two units.
SpikeSorter.jl	Julia	hidden markov model	spike width, trough to valley ratio	hidden markov model	No	No	No		Algorithm described in Spike sorting with hidden Markov models
SpikeSorting.jl	Julia	raw signal threshold, power, nonlinear energy, alignment	PCA	OSort-style template matching	Yes?	No	No		Many options planned; see documentation
spyke	Python	raw signal threshold with alignment	PCA, ICA	gradient ascent (mean-shift variant)	No	No	Yes	Spike sorting for polytrodes: a divide and conquer approach, Python for large-scale electrophysiology	GUI
SpyKING Circus	Python	raw signal threshold + iterative template matching	PCA	local density clustering (Rodriguez & Laio) + template matching	No	Yes	Yes	Fast and accurate spike sorting in vitro and in vivo for up to thousands of electrodes
trisdesclous	Python	raw signal threshold with alignment	PCA	EM GMM, k-means	No	No	No
Wave_clus	MATLAB	raw signal threshold with alignment	wavelets + Lillifors test	superparamagnetic	No	No	No	Unsupervised spike detection and sorting with wavelets and superparamagnetic clustering