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NWB 2.0 Data Format Plugin for the Open Ephys GUI
- Josh Siegle (Allen Institute)
- Pavel Kulik (Allen Institute)
The Open Ephys GUI provides a modular interface for acquiring multichannel extracellular electrophysiology data. Its plugin architecture makes it straightforward to add new formats for recording data. The GUI currently supports writing in NWB 1.0 format, which is now deprecated. We plan to create a new plugin that can stream data directly to NWB 2.0 files.
- Generate HDF5 files from Open Ephys that are compatible with the NWB 2.0 spec
- Stream continuous and event data into the file (ideally from a Neuropixels probe)
- Read data saved with Open Ephys using the Python or Matlab API
Approach and Plan
- Find an existing NWB 2.0 file containing raw ephys data, which we will attempt to replicate from Open Ephys.
- Using the current
NWBFormat plugin as a starting point, update the
NWBFile::createFileStructure() method to match the example file.
- Ensure that the
writeTimestamps methods are compatible with the new file structure.
- Build the new plugin and stream 384 channels of data from a Neuropixels probe.
- Confirm that the resulting file can be read with existing NWB tools, such as the Matlab or Python SDK.
Progress and Next Steps
Background and References