bluecellulab.tools

Module for calculating certain properties of Neurons.

Functions

calculate_SS_voltage(template_path, ...[, ...])

Calculate the steady state voltage at a certain current step.

calculate_SS_voltage_subprocess(...[, ...])

Subprocess wrapper of calculate_SS_voltage.

calculate_input_resistance(template_path, ...)

Calculate the input resistance at rest of the cell.

calculate_max_thresh_current(cell[, ...])

Calculate the upper bound threshold current.

calculate_rheobase(cell[, ...])

Calculate the rheobase by first computing the upper bound threshold current.

check_empty_topology()

Return true if NEURON simulator topology command is empty.

compute_memodel_properties(cell[, ...])

Compute the threshold current and the input resistance of the cell.

detect_hyp_current(template_path, ...)

Search current necessary to bring cell to -85 mV.

detect_spike(voltage[, step_thresh])

Detect if there is a spike in the voltage trace.

detect_spike_step(template_path, ...[, ...])

Detect if there is a spike at a certain step level.

detect_spike_step_subprocess(template_path, ...)

Detect if there is a spike at a certain step level.

holding_current(v_hold, cell_id, circuit_path)

Calculate the holding current necessary for a given holding voltage.

holding_current_subprocess(v_hold, ...)

Subprocess wrapper of holding_current.

resolve_source_nodes(source, report_type, ...)

search_hyp_current(template_path, ...)

Search current necessary to bring cell to -85 mV.

search_threshold_current(template_name, ...)

Search current necessary to reach threshold.

template_accepts_cvode(template_name)

Return True if template_name can be run with cvode.

validate_section_and_segment(cell, ...)

Validate a single section and segment position.
bluecellulab.tools.calculate_SS_voltage(template_path, morphology_path, template_format, emodel_properties, step_level, check_for_spiking=False, spike_threshold=-20.0, section='soma[0]', segx=0.5)[source]

Calculate the steady state voltage at a certain current step.

Parameters:

  • template_path (str | Path)

  • morphology_path (str | Path)

  • template_format (str)

  • emodel_properties (EmodelProperties | None)

  • step_level (float)

  • section (str)

  • segx (float)

Return type:

float

bluecellulab.tools.calculate_SS_voltage_subprocess(template_path, morphology_path, template_format, emodel_properties, step_level, check_for_spiking, spike_threshold, section='soma[0]', segx=0.5)[source]

Subprocess wrapper of calculate_SS_voltage.

This code should be run in a separate process. If check_for_spiking is True, this function will return None if the cell spikes from 100ms to the end of the simulation indicating no steady state was reached.

Parameters:

  • template_path (str | Path)

  • morphology_path (str | Path)

  • template_format (str)

  • emodel_properties (EmodelProperties | None)

  • step_level (float)

  • check_for_spiking (bool)

  • spike_threshold (float)

  • section (str)

  • segx (float)

Return type:

float

bluecellulab.tools.calculate_input_resistance(template_path, morphology_path, template_format, emodel_properties, current_delta=-0.02, section='soma[0]', segx=0.5)[source]

Calculate the input resistance at rest of the cell.

Parameters:

  • template_path (str | Path)

  • morphology_path (str | Path)

  • template_format (str)

  • emodel_properties (EmodelProperties | None)

  • current_delta (float)

  • section (str)

  • segx (float)

Return type:

float

bluecellulab.tools.calculate_max_thresh_current(cell, threshold_voltage=-20.0, section='soma[0]', segx=0.5)[source]

Calculate the upper bound threshold current.

Parameters:

  • cell (bluecellulab.cell.Cell) – The initialized cell model.

  • threshold_voltage (float, optional) – Voltage threshold for spike detection. Default is -20.0 mV.

  • section (str, optional) – The section where current is injected.

  • segx (float, optional) – Fractional location within the section for current injection.

Returns:

The upper bound threshold current.

Return type:

float

bluecellulab.tools.calculate_rheobase(cell, threshold_voltage=-20.0, threshold_search_stim_start=300.0, threshold_search_stim_stop=1000.0, section='soma[0]', segx=0.5)[source]

Calculate the rheobase by first computing the upper bound threshold current.

Parameters:

  • cell (bluecellulab.cell.Cell) – The initialized cell model.

  • threshold_voltage (float, optional) – Voltage threshold for spike detection. Default is -20.0 mV.

  • threshold_search_stim_start (float, optional) – Start time for threshold search stimulation (in ms). Default is 300.0 ms.

  • threshold_search_stim_stop (float, optional) – Stop time for threshold search stimulation (in ms). Default is 1000.0 ms.

  • section (str, optional) – The section where current is injected.

  • segx (float, optional) – Fractional location within the section for current injection.

Returns:

The rheobase current.

Return type:

float

bluecellulab.tools.check_empty_topology()[source]

Return true if NEURON simulator topology command is empty.

Return type:

bool

bluecellulab.tools.compute_memodel_properties(cell, spike_threshold_voltage=-30, v_init=-80.0, celsius=34.0)[source]

Compute the threshold current and the input resistance of the cell.

Parameters:

  • cell (Cell) – The cell model to compute properties for.

  • spike_threshold_voltage (float, optional) – Voltage threshold for spike detection. Default is -30 mV.

  • v_init (float, optional) – Initial membrane potential. Default is -80 mV.

  • celsius (float, optional) – Temperature in Celsius. Default is 34.0 C.

bluecellulab.tools.detect_hyp_current(template_path, morphology_path, template_format, emodel_properties, target_voltage)[source]

Search current necessary to bring cell to -85 mV.

Compared to using NEURON’s SEClamp object, the binary search better replicates what experimentalists use

Parameters:

  • template_path (str | Path)

  • morphology_path (str | Path)

  • template_format (str)

  • emodel_properties (EmodelProperties | None)

  • target_voltage (float)

Return type:

float

bluecellulab.tools.detect_spike(voltage, step_thresh=-20.0)[source]

Detect if there is a spike in the voltage trace.

Parameters:

  • voltage (ndarray)

  • step_thresh (float)

Return type:

bool

bluecellulab.tools.detect_spike_step(template_path, morphology_path, template_format, emodel_properties, hyp_level, inj_start, inj_stop, step_level, section='soma[0]', segx=0.5, step_thresh=-20.0)[source]

Detect if there is a spike at a certain step level.

Parameters:

  • template_path (str | Path)

  • morphology_path (str | Path)

  • template_format (str)

  • emodel_properties (EmodelProperties | None)

  • hyp_level (float)

  • inj_start (float)

  • inj_stop (float)

  • step_level (float)

  • section (str)

  • segx (float)

  • step_thresh (float)

Return type:

bool

bluecellulab.tools.detect_spike_step_subprocess(template_path, morphology_path, template_format, emodel_properties, hyp_level, inj_start, inj_stop, step_level, section='soma[0]', segx=0.5, step_thresh=-20.0)[source]

Detect if there is a spike at a certain step level.

Parameters:

  • template_path (str | Path)

  • morphology_path (str | Path)

  • template_format (str)

  • emodel_properties (EmodelProperties | None)

  • hyp_level (float)

  • inj_start (float)

  • inj_stop (float)

  • step_level (float)

  • section (str)

  • segx (float)

  • step_thresh (float)

Return type:

bool

bluecellulab.tools.holding_current(v_hold, cell_id, circuit_path, enable_ttx=False)[source]

Calculate the holding current necessary for a given holding voltage.

Parameters:

  • v_hold (float)

  • cell_id (int | tuple[str, int])

  • circuit_path (str | Path)

Return type:

Tuple[float, float]

bluecellulab.tools.holding_current_subprocess(v_hold, enable_ttx, cell_kwargs)[source]

Subprocess wrapper of holding_current.

bluecellulab.tools.search_hyp_current(template_path, morphology_path, template_format, emodel_properties, target_voltage, min_current, max_current)[source]

Search current necessary to bring cell to -85 mV.

Parameters:

  • template_path (str | Path)

  • morphology_path (str | Path)

  • template_format (str)

  • emodel_properties (Optional[EmodelProperties])

  • target_voltage (float)

  • min_current (float)

  • max_current (float)

Return type:

float

bluecellulab.tools.search_threshold_current(template_name, morphology_path, template_format, emodel_properties, hyp_level, inj_start, inj_stop, min_current, max_current, current_precision=0.01, section='soma[0]', segx=0.5, step_thresh=-20.0)[source]

Search current necessary to reach threshold.

Parameters:

  • template_name (str | Path)

  • morphology_path (str | Path)

  • template_format (str)

  • emodel_properties (EmodelProperties | None)

  • hyp_level (float)

  • inj_start (float)

  • inj_stop (float)

  • min_current (float)

  • max_current (float)

  • current_precision (float)

  • section (str)

  • segx (float)

  • step_thresh (float)

bluecellulab.tools.template_accepts_cvode(template_name)[source]

Return True if template_name can be run with cvode.

Parameters:

template_name (str | Path)

Return type:

bool

bluecellulab.tools.validate_section_and_segment(cell, section_name, segment_position)[source]

Validate a single section and segment position.

Parameters:

  • cell (Cell) – The cell model to validate against.

  • section_name (str) – The name of the section to validate (e.g., ‘soma’, ‘axon[1]’).

  • segment_position (float) – The position within the section (e.g., 0.5 for the middle).

Raises:

ValueError – If the section or position is invalid.