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NWB for Neuropixels Experiments
Key Investigators
Project Description
We will represent high-density exctracellular electrophysiology (ecephys) data in NWB.
Objective
- Flexible representation of spike-sorting outputs
- Build analogous functionality for Ophys data (DM).
Approach and Plan
- Identify and obtain a pool of raw datasets.
- Write these datasets to NWB files (and read them back!).
- Ensure that common features of these datasets are supported by the core
NWB namespace or an extension.
- Document the process of writing ecephys data to NWB.
Progress
- Implemented generic unit metrics group (for storing snr/peak amplitudes) in core. See pr #435
- Packaged kilosort/phy outputs with pynwb. See notebook
Next Steps
- We need to associate mean/std waveforms and electrode table regions with UnitTimes in core. See issue #431
- Create a tutorial for packaging Kilosort/phy outputs with pynwb
Functionality Table
A table of things that we want to write to NWB files. Please fill in/edit entries! Columns are:
- functionality: short description
- tools supported: if the functionality is kilosort-specific, for instance
- PyNWB class: the PyNWB class(es) that currently supports this feature (or the closest match).
- notes: additional information.
| 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? |
Illustrations
Background and References
- Forum: https://github.com/orgs/NeurodataWithoutBorders/teams/neuropixels/discussions
- Source code: https://github.com/YourUser/YourRepository
- Documentation: https://link.to.docs
- Test data: https://link.to.test.data