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NWB for Neuropixels Experiments

Key Investigators

Project Description

We will represent high-density exctracellular electrophysiology (ecephys) data in NWB.


  1. Flexible representation of spike-sorting outputs
  2. Build analogous functionality for Ophys data (DM).

Approach and Plan

  1. Identify and obtain a pool of raw datasets.
  2. Write these datasets to NWB files (and read them back!).
  3. Ensure that common features of these datasets are supported by the core NWB namespace or an extension.
  4. Document the process of writing ecephys data to NWB.


Next Steps

Functionality Table

A table of things that we want to write to NWB files. Please fill in/edit entries! Columns are:

functionality tools supported PyNWB class notes
Sorted units all ecephys.Clustering misc.UnitTimes NB: UnitTimes was recently refactored (pynwb pr #382). Doc fixes outstanding (nwb-schema issue #117)
Event tiimes all ecephys.Clustering misc.UnitTimes  
Unitwise metrics (peak amplitude, snr, classifications) all ecephys.Clustering pr #435 Created a new UnitMetrics class to handle unitwise metrics generically
Eventwise metrics (amplitude, PCs) all ecephys.FeatureExtraction (?) These are likely to be lab specific. A solution based on MultiContainerInterface seems sensible
Unit waveforms all ecephys.ClusterWaveforms Currently, it’s not clear how to relate waveforms to unit IDs. issue #431
LFP all ecephys.LFP ecephys.ElectricalSeries  
Current Source Density all ecephys.ElectricalSeries (?) not sure if the dimensionality works. Should attach to LFP?


Background and References