Export subject to NWB

NWB_Packaging_Subject_Capsule

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:

• a base valid NWB file to append the ephys data to
• the raw data
• (optional) a list of json files produced by the aind-ephys-job-dispatch process

If no JSON files are provided, the capsule will assume the raw data is in the AIND ephys format. When JSON files are provided, the capsule will use this information to load the raw and LFP data.

Parameters

The code/run script takes the following arguments:

  --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.