single_cell_parser ❭ cell ❭ Cell

Cell¶

class single_cell_parser.cell.Cell¶

Cell object providing API to the NEURON hoc interface.

This class contains the neuron cell morphology, biophysical parameters, and simulation data of single-cell simulations. The main purpose is to be a dataclass containing this information, but not to create or configure it on its own. Its attributes are set by CellParser.

See also

This is not the same class as singlecell_input_mapper.singlecell_input_mapper.cell.Cell. This class concerns itself with providing API to NEURON, not with mapping input to the cell.

Attributes:¶

hoc_path¶

Path to the hoc file containing the cell morphology.

Type:¶: str

id¶

ID of the cell (often unused).

Type:¶: str | int, optional

soma¶

The soma section of the cell.

Type:¶: PySection

tree¶

NEURON SectionList containing all sections of the cell.

Type:¶: neuron.h.SectionList

branches¶

maps the section ID (str) of the root section of each dendritic subtree to its corresponding section list (neuron.h.SectionList).

Type:¶: dict

structures¶

All sections, aggregated by label (e.g. Dendrite, ApicalDendrite, ApicalTuft, Myelin…). Keys are labels (str), values are lists of PySection objects.

Type:¶: Dict[PySection]

sections¶

List of PySection objects. First element is the soma. Each section contains recorded data (if any was recorded, e.g. membrane voltage): a 2D array where axis 0 is segment number, and axis 1 is time.

Type:¶: List[PySection]

synapses¶

a dictionary of lists of single_cell_parser.synapse.Synapse objects

Type:¶: dict

E¶

Default resting membrane potential. Defaults to -70.0

Type:¶: float

changeSynParamDict¶

dictionary of network parameter sets with keys corresponding to time points. Allows automatic update of parameter sets according to their relative timing.

Type:¶: dict

tVec¶

a hoc Vector recording time.

Type:¶: neuron.h.Vector

neuron_param¶: The Cell parameters.

section_adjacency_map¶

maps each section (by ID) to its parent sections and children sections.

Type:¶: dict

Methods:¶

`re_init_cell`(replayMode)	Re-initialize for next simulation run.
`record_range_var`(var, mech)	Record a range mechanism in all sections.
`get_range_var_conductances`(density)	Get the conductances of each section, categorized by range variable and segment.
`distance_between_pts`(sec1, x1, sec2, x2)	Computes the path length between two points.
`distance_to_soma`(sec, x)	Computes the path length between the soma and a specified point.
`max_distance`(label)	Computes maximum path length to soma of all branches with label `label`
`add_synapse`(secID, ptID, ptx, preType, postType)	Add a `Synapse` to the cell object.
`remove_synapses`(preType)	Remove synapses from the cell object of type `preType`.
`init_time_recording`()	Initialize the NEURON time vector for recording.
`get_synapse_activation_dataframe`(max_spikes, sim_trial_index)	Get a Synapse activation dataframe.
`get_section_adjacancy_map`()	Generates a map that shows which sections are connected to which sections.