EMUsort settings

EMUsort (O’Connell et al. 2026): high-density intramuscular arrays, motor units

dspk sort emusort [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
• --templates <TEMPLATES>
  Predefined universal templates (.npz with wPCA, wTEMP) when –templates-from-data false
• --show-config
  Print every setting of the run and exit
• --nt <NT>: default 61
  Samples per waveform (odd); 61 is 2 ms at 30 kHz
• --nt-ms <NT_MS>
  Waveform length in ms (overrides –nt: rounded to an odd sample count for the recording)
• --nt0min <NT0MIN>
  Sample a waveform’s trough is aligned to; default: int(20 · nt / 61)
• --th-universal <TH_UNIVERSAL>: default 9
  Universal-template detection threshold (whitened σ)
• --th-learned <TH_LEARNED>: default 8
  Learned-template matching threshold (whitened σ)
• --th-single-ch <TH_SINGLE_CH>: default 6 9 12 15
  Single-channel thresholds of the clips templates are learned from (whitened σ), comma-separated
• --templates-from-data <TEMPLATES_FROM_DATA>: default true, one of true, false
  Learn the universal templates from the recording (false: Kilosort4’s predefined ones, from –templates or downloaded through dspk-hub)
• --n-templates <N_TEMPLATES>: default 9
  Universal templates learned
• --n-pcs <N_PCS>: default 9
  Principal components per channel
• --nskip <NSKIP>: default 2
  Every nskip-th batch is used for template learning
• --do-car <DO_CAR>: default false, one of true, false
  Common average reference before filtering
• --do-bandpass <DO_BANDPASS>: default true, one of true, false
  Butterworth band-pass (order 3 per edge, zero phase); false: no Butterworth
• --bandpass-low-hz <BANDPASS_LOW_HZ>: default 300
  Lower band edge (Hz)
• --bandpass-high-hz <BANDPASS_HIGH_HZ>: default 5000
  Upper band edge (Hz), below Nyquist; 0: no upper edge (a high-pass)
• --do-notch <DO_NOTCH>: default false, one of true, false
  Line-noise notch after the band
• --notch-hz <NOTCH_HZ>: default 60
  Notch frequency (Hz; 50 outside the Americas)
• --notch-q <NOTCH_Q>: default 30
  Quality factor of the notch (bandwidth = notch / Q)
• --whitening-range <WHITENING_RANGE>: default 32
  Channels in each local whitening neighbourhood
• --batch-size <BATCH_SIZE>: default 60000
  Samples per batch
• --max-peels <MAX_PEELS>: default 50
  Matching-pursuit rounds per window
• --global-merges <GLOBAL_MERGES>: default true, one of true, false
  Merge units whose waveforms are alike and whose spikes are mutually refractory
• --merge-similarity <MERGE_SIMILARITY>: default 0.5
  Waveform similarity (correlation over lags) a pair needs to be tested for a merge
• --duplicate-spike-ms <DUPLICATE_SPIKE_MS>: default 0.25
  A unit’s spikes within this many ms of its previous spike are removed (0 keeps them)
• --reproducible <REPRODUCIBLE>: default true, one of true, false
  Same input on the same device gives the same spikes
• --remove-channel-delays <REMOVE_CHANNEL_DELAYS>: default true, one of true, false
  Estimate and remove per-channel delays (up to 2 ms)
• --remove-spike-outliers <REMOVE_SPIKE_OUTLIERS>: default true, one of true, false
  Remove outlier clips (HDBSCAN) before learning the universal templates
• --hdbscan-min-cluster-size <HDBSCAN_MIN_CLUSTER_SIZE>: default 20
  HDBSCAN min_cluster_size of the outlier removal