SpikeSort 3D

Convenient and Fast Spike Waveform Classification

SpikeSort 3D is an online and offline spike waveform-to-cell classification tool. SpikeSort 3D is integrated with Cheetah via NetCom for online spike sorting, and also runs as a stand-alone offline program for spike classification.

Fast, smooth 3D display manipulation enables users to quickly identify and isolate clusters/cells. Manual clustering modes include convex hulls in three dimensional space, rectangular boundaries, and waveform templates on raw spike waveforms. Clusters can also be defined in any arbitrary 3D view of feature space.

Waveform parameter calculations include standard measures such as Peak, Valley, Area and Energy, and advanced measures such as Principal Component Analysis.

Spike files may be saved with new assignments intact, cluster definitions may be saved for later use, and timestamp files are created for importing clustered data into virtually any analysis software.

SpikeSort 3D features:
  • Principal component analysis
  • Cluster quality measures – isolation distance and L-ratio
  • Automatic sorting via a KlustaKwik interface
  • Up to 8 features calculated for each spike
  • Inter-spike interval and average waveform displays
  • Same program and UI for online or offline classification
  • Fast graphics drawing - even for million spikes data sets
  • Optimized displays using OpenGL technology
  • Spike file size limited only by system memory
  • Manual cutting using rectangles, convex hulls or user-input waveform templates


Users may choose options for manual clustering, including convex polygons and rectangular boundaries in feature space, and waveform templates (window discriminator) on raw spike data. Data clusters can also be defined in any arbitrary 3 dimensional view of feature space. Waveform parameter calculations include standard measures, from Peak, Valley, Area and Energy to advanced measures such as Principal Component Analysis.



Spike files may be saved with new assignments intact, cluster definitions may be saved for later use, and timestamp files may be created for importing clustered data into virtually any analysis software.

SS3D is compatible with SNAP Sorter auto-clustering software. SNAP saves you time and effort, eliminating hours of manual spike sorting on each data set. SNAP Sorter:

  • Classifies and sorts over 100K tetrode spikes in only several minutes
  • Batch processes all tetrodes’ spike files in a data set
  • Provides results before next day’s recording session
  • Provides better results than manual cluster cutting!

SNAP does Spike Sorting so YOU don’t have to!