visualize ❭ dendrogram ❭ _DendrogramSynapseStatistics

_DendrogramSynapseStatistics¶

class visualize.dendrogram._DendrogramSynapseStatistics(dendrogram_db, cell, colormap_synapses=None)¶

Compute synapse statistics for a Cell object.

Synaptic statistics include the total amount of synapses binned by soma distance, both unnormalized, as well as normalized by total amount of dendritic length.

Parameters:¶

• dendrogram_db (list) – A list of _DendrogramSection objects.

• cell (Cell) – The cell object.

• colormap_synapses (dict) – A dictionary mapping color to synapse types. The keys must match the synapse types in the dendrogram. Missing keys will be omitted from the visualization alltogether. Default: None (plot all synapses in black).

Attributes:¶

dendrogram_db¶

A list of _DendrogramSection objects.

Type:¶

list

cell¶

The cell object.

Type:¶

Cell

colormap_synapses¶

A dictionary mapping color to synapse types. The keys must match the synapse types in the dendrogram. Missing keys will be omitted from the visualization alltogether. Default: None (plot all synapses in black).

Type:¶

dict

bins¶

The bins of the synapse density histogram.

Type:¶

np.array

synapse_density¶

The synapse density histogram, i.e. the amount of synapses within a range of soma distance.

Type:¶

np.array

synapse_density_apical¶

The synapse density histogram for apical dendrites.

Type:¶

np.array

synapse_density_basal¶

The synapse density histogram for basal dendrites.

Type:¶

np.array

synapse_statistics¶

A dictionary of synapse statistics

Type:¶

dict

Methods:¶

_add_synapses()	Add synapses to the dendrogram sections.
get_number_of_synapses_in_bin(min_, max_, select, label)	Get the number of synapses in a certain bin of soma distance.
_compute_synapse_hist(binsize)	Compute the synapse density histogram.
_compute_synapse_statistics()	Compute the synapse statistics.
_plot_synapse_density_hist(ax, xlim, binsize)	Plot the synapse density histogram on an matplotlib.axes.Axes object.
_plot_synapse_hist(ax, dendrite_density)	Plot the synapse histogram on an matplotlib.Axes object.
_plot_synapses_dendrogram_overlay(ax)	Plot the synapses on the dendrogram.
plot(ax)	Plot the synapse statistics