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Cell Utility Commands

The util cell commands provide tools for building, tuning, and identifying properties of single cell models.

Many of the following examples can be tested using the example data in docs/examples/cli/single_cell. To test the commands first make sure you have these example files, then set your terminal to be in this single_cell directory. 

bmtool util cell --help

Shared Options

Most cell commands allow overriding the cell's location and loading parameters:

  • --hoc-folder: Override the HOC location (defaults to current directory or config).
  • --mod-folder: Override the MOD file location (defaults to current directory or config).
  • --template: Specify the NEURON template name.
  • --hoc: Specify a single HOC file to load (when multiple files are present).

Interactive Tuning (GUI)

Open interactive NEURON GUI windows for visual tuning of cell behavior and F-I curves.

Cell Tuner

Open a general-purpose tuning interface for testing different stimulation protocols.

# Quick start using "easy" mode
bmtool util cell --template ET_Cell --hoc-folder . --mod-folder ./modfiles tune --easy

For advanced users, the --builder mode allows you to construct custom interfaces with specific widgets and plots: 

bmtool util cell --template ET_Cell --hoc-folder . --mod-folder ./modfiles tune --builder

FI Curve Interface

Open an interface dedicated to calculating FI curves (Frequency vs. Current) and passive property summaries.

bmtool util cell --template ET_Cell --hoc-folder . --mod-folder ./modfiles fi

Characterization (Passive & ZAP)

These commands allow for quick, non-interactive characterization of cell properties from the command line.

Passive Properties

Calculate \(V_{rest}\), \(R_{in}\) (input resistance), and \(\tau\) (membrane time constant).

# Calculate passive properties with default values
bmtool util cell --template ET_Cell --hoc-folder . --mod-folder ./modfiles passive --plot

Options: - --inj-amp: Injection amplitude in pA (default: -100). - --inj-delay: Start time of injection (default: 200ms). - --inj-dur: Duration of injection (default: 1000ms). - --tstop: Total simulation time (default: 1200ms). - --method: simple, exp, or exp2 for \(\tau\) fitting. - --plot: Display/Save the membrane potential trace.

ZAP (Impedance & Resonance)

Calculate frequency-dependent impedance and resonant frequency using a chirp current injection.

# Run a ZAP simulation from 0 to 100 Hz
bmtool util cell --template ET_Cell --hoc-folder . --mod-folder ./modfiles zap --plot

Options: - --inj-amp: Chirp amplitude in pA (default: 100.0). - --fstart: Start frequency in Hz (default: 0.0). - --fend: End frequency in Hz (default: 100.0). - --inj-delay: Injection delay in ms (default: 200.0). - --inj-dur: Chirp duration in ms (default: 1000.0). - --tstop: Total simulation time in ms (default: 1200.0). - --plot: Display/Save the ZAP results.

VHalf Segregation (Alturki et al. 2016)

The VHalf Segregation tool provides an automated interface to simplify tuning by separating channel activation (V1/2). This implements the methodology described in Alturki et al. (2016).

# Launch the interactive wizard
bmtool util cell vhseg

Command-line mode (skipping the wizard): 

bmtool util cell --template CA3PyramidalCell vhseg --othersec dend[0],dend[1] \
  --infvars inf_im --segvars gbar_im --gleak gl_ichan2CA3 --eleak el_ichan2CA3