SpyKING CIRCUS 2 settings

SpyKING CIRCUS 2 (SpikeInterface): published defaults

dspk sort spykingcircus2 [OPTIONS] --output <OUTPUT> <RECORDING>

Arguments

• <RECORDING>
  Recording (SpikeGLX .bin / .cbin, raw .bin + JSON .meta, NWB, Zarr)

Settings

• --source <SOURCE>
  Source within the file (an id dspk-cli open lists); default: the largest electrical one
• --probe <PROBE>: one of neuropixels1, neuropixels2, tetrode, utah, hdemg4x8, hdemg8x8
  Probe preset; default: the geometry the recording carries (SpikeGLX), else an error
• --probe-file <PROBE_FILE>
  Probe file (.json: probeinterface or Kilosort 4) saying which channel each contact is wired to: the data is read in contact order (unconnected contacts left out), with its geometry
• --progress <PROGRESS>: default bar, one of bar, json
  How progress is reported: bar (on stderr) or json (one JSON object per line on stdout: progress events, then done or error; for programs running this one)
• --channel-map <CHANNEL_MAP>
  Channel map (.toml / .json, pairs under remap) applied after the probe: channels reordered, dropped, renamed; the geometry follows them
• --pitch-um <PITCH_UM>: default 8000
  Electrode pitch of HD-EMG grid presets (µm)
• --start-sec <START_SEC>: default 0
  Start of the part to process (s)
• --duration-sec <DURATION_SEC>
  Length of the part to process (s); default: to the end
• -o, --output <OUTPUT>
  Output folder or store
• --format <FORMAT>
  Output format; default: from the name (.nwb.zarr → nwb, other .zarr → zarr, else phy)
  • phy: Phy / Kilosort folder (.npy arrays, .tsv tables)
  • zarr: dspk .sorting.zarr store
  • nwb: NWB /units table in a .nwb.zarr store
• --show-config
  Print every setting of the run and exit