Converts continuous data from raw NPX/NPX2 format (75% compression ratio) to .dat files required for spike sorting and other downstream analysis.
Reads event times from the NPX/NPX2 file and writes them as .npy files.
Converts the settings.xml file for an experiment into a JSON file with parameters such as sample rate and bit volts for each channel.
Note: The NPX format is no longer used by Open Ephys (or any other software), so this module can safely be skipped.
The NpxExtractor executable (Windows only) can be found in the NpxExtractor\Release folder.
python -m ecephys_spike_sorting.modules.extract_from_npx --input_json <path to input json> --output_json <path to output json>
Two arguments must be included:
- The location of an existing file in JSON format containing a list of paths and parameters.
- The location to write a file in JSON format containing information generated by the module while it was run.
See the _schemas.py file for detailed information about the contents of the input JSON.
- NPX file : Written by Open Ephys (https://github.com/open-ephys/plugin-GUI). Contains all of the data recorded from one or more Neuropixels probes.
- settings.xml : Written by Open Ephys. Contains information about the signal chain that was used for the experiment.
- continuous.dat : Continuous data (1 file each for LFP and AP band)
- lfp_timestamps.npy : Timestamps for LFP samples
- ap_timestamps.npy : Timestamps for AP samples
- channel_states.npy : Channels on which each event was recording
- event_timestamps.npy : Timestamps for each event
- open-ephys.json : Parameters for data acquistion.