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OpenReadout

Spike features for a folder of recordings

Use this when you have a folder of patch-clamp recordings (ABF, ATF, NWB) and want one table of their features: spike counts, rheobase, f–I slope, input resistance for current clamp, or holding current and access resistance for voltage clamp.

Run it

$ openreadout batch ephys-features cells/ --set rows=cell --fields clamp_mode,spike_count_total,rheobase_pa,fi_slope_hz_per_pa,input_resistance_mohm
3 data sets (3 ok, 0 failed)
path                                 format  clamp_mode     spike_count_total  rheobase_pa  fi_slope_hz_per_pa  input_resistance_mohm
───────────────────────────────────  ──────  ─────────────  ─────────────────  ───────────  ──────────────────  ─────────────────────
cells/pyabf-171116sh-0018.abf        abf     current_clamp                117           50              0.0655               104.1564
cells/pyabf-190619b-0003.abf         abf     current_clamp                117          120             -0.0538               224.0087
cells/pyabf-2019-07-24-0055-fsi.abf  abf     current_clamp                948           25              0.3717               176.8225

cells/ holds three public current-clamp recordings from the pyABF sample data (MIT): 171116sh_0018.abf, 190619b_0003.abf and 2019-07-24 0055 fsi.abf, a fast-spiking interneuron. Each has a series of current steps that drive the cell from silence to repetitive firing. The output on this page is real.

What it tells you

  • Each row is one recording (rows=cell). --fields keeps the table narrow; without it you also get max_firing_rate_hz, tau_ms, sag_ratio and resting_mv. Voltage-clamp files give holding_current_pa, access_resistance_mohm and membrane_resistance_mohm instead.
  • clamp_mode is decided from the units: a voltage channel with a current command is current clamp, a current channel with a voltage command is voltage clamp.
  • Rheobase is the smallest step that makes the cell fire, and the f–I slope is fitted over the steps that do. A negative slope means the rate falls at the larger steps: 190619b_0003 fires 98 spikes at 240 pA and 1 at 420 pA (--csv fi shows the curve), so look at it before you average slopes.
  • Check the units before you trust a number. If samples are implausible for the channel’s unit (a current channel labelled A that holds values of a few units, say), the report adds a note naming the likely unit. openreadout info FILE shows each channel’s unit.
  • A file that cannot be analyzed becomes a row with error and error_code, and the run carries on.

Variations

One row per sweep or per spike

rows=sweep (the default) gives one row per sweep, with the stimulus window and level, spike_count, firing_rate_hz, first_spike_latency_ms, the ISI measures and the passive or test-pulse values. rows=spike gives one row per action potential, with threshold, amplitude, half-width and AHP.

One file

Terminal window
openreadout analyze ephys-features cell.abf
openreadout analyze ephys-features cell.abf --csv sweeps > sweeps.csv
openreadout analyze ephys-features cell.abf --csv fi > fi.csv

--csv prints one tidy table (sweeps, spikes or fi) instead of the report. A spike must cross −20 mV (--peak-threshold), and its onset is where dV/dt reaches 10 V/s (--dvdt-threshold). --sweeps 0,3,5-9 limits the sweeps. Stimulus steps, and so rheobase and the f–I curve, come from ABF epoch tables only.

Grouped by genotype

Terminal window
openreadout batch ephys-features cells/ -r --set rows=cell \
    --sample-sheet genotypes.csv --by genotype -o cells.parquet

OpenReadout picks the join key itself (usually the file name) and reports it, and --by adds n, mean, SD, SEM and median per group. --set peak_threshold_mv=-30 passes an option; the names are those of the MCP tool. Writing a CSV of the table above:

$ openreadout batch ephys-features cells/ --set rows=cell -o cells.csv
...
wrote cells.csv (3 rows × 13 columns, csv, 699 bytes, verified=true)

From an assistant

The MCP tool is openreadout_analyze with kind: "ephys-features" and options trace, channel, sweeps, peak_threshold_mv, dvdt_threshold and max_spikes. For a folder, openreadout_batch takes measure: "ephys-features" with the same options plus rows.

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