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Spike sorting Review
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spike-sorting.md

Spike sorting packages

Name Platform Notes
kilosort MATLAB + drift correction, GPU
mountainsort
  2. mountainsort
  3. wave_clus wavelets + super-paramagnetic clustering
  4. FAST
  5. spikeinterface
  6. spykes
  7. spykesML ML algorithms for spike prediction
  8. klusta automatic spike sorting
  9. nerds blind deconv. in MATLAB 10.BinaryPursuitSpikeSorting
  10. mksort
  11. moksm Kalman filters + EM
  12. bpsort binary pursuit
  13. LDA-GMM_SpikeSort discrminative subspace learning

Fundamentals

spike sorting is typically a blind source seperation problem

Historical computational workflows

preprocessing

  1. High pass filter to remove LFP
  2. Spatial filtering/whiteneing to maybe remove extinisic noise
  3. Thresholding to identify putative spikes
  4. Cut out snippets

Dim Red

  1. PCA/t-SNE

Clustering

  1. Density-based clsutering

Template Matching

This is to solve the problem of mulitple neurons firing at the same time, and their waveforms superimposing. The waveforms typically summate because the extracellular medium is mostly conductive.

Datasets to play with

Allen Brain Obs. Neuropixels dataset

Talks

  1. Alessio Buccino - spikeinterface
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