Export ecephys to NWB

NWB Packaging Ecephys

Description

This capsule is designed to append device, electrodes, LFP and raw (optional) electrical series information to an existing NWB file.

Inputs

The data/ folder must include:

• the raw data in any supported format (e.g. AIND ephys format, OpenEphys, SpikeGLX, etc.)
• (optional) a list of json files produced by the aind-ephys-job-dispatch process

If the input data is already in NWB format, the capsule will simply start from the existing NWB file and append the ecephys data. If in another format, the capsule will look for the subject.json and data_description.json files in the data/ folder to extract subject and session metadata. If these files are not found, the capsule will create mock subject and session metadata.

Parameters

The code/run script takes the following arguments:

  --backend {pynwb,hdmf}
                        Backend to use for NWB writing (if pipeline 'input' is not NWB)
  --stub                Write a stub version for testing
  --stub-seconds STUB_SECONDS
                        Duration of stub recording
  --skip-lfp            Whether to write LFP electrical series
  --write-raw           Whether to write RAW electrical series
  --lfp_temporal_factor LFP_TEMPORAL_FACTOR
                        Ratio of input samples to output samples in time. Use 0 or 1 to keep all samples. Default is 2.
  --lfp_spatial_factor LFP_SPATIAL_FACTOR
                        Controls number of channels to skip in spatial subsampling. Use 0 or 1 to keep all channels. Default is 4.
  --lfp_highpass_freq_min LFP_HIGHPASS_FREQ_MIN
                        Cutoff frequency for highpass filter to apply to the LFP recorsings. Default is 0.1 Hz. Use 0 to skip filtering.
  --surface_channel_agar_probes_indices SURFACE_CHANNEL_AGAR_PROBES_INDICES
                        Index of surface channel (e.g. index 0 corresponds to channel 1) of probe for common median referencing for probes in agar. Pass in as JSON
                        string where key is probe and value is surface channel (e.g. "{'ProbeA': 350, 'ProbeB': 360}")

Output

The output of this capsule is a set of NWB files in the results/ folder named associated with different experiments/blocks and segments.