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:¶

SectionList

branches¶

maps the section ID (str) of the root section of each dendritic subtree to its corresponding section list (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 NEURON Vector recording time.

Type:¶

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.