❭ API reference ❭ singlecell_input_mapper ❭

singlecell_input_mapper¶

Create an empirically constrained dense connectome model with presynaptic activity.

This package provides classes and methods to create a dense connectome model with defined activity patterns. It can be largely divided in two parts: Connectivity and Activity. This data is generated or read directly from empirical data sources, and added to a single Network parameters.

Connectivity¶

singlecell_input_mapper.map_singlecell_inputs is responsible for assigning synapses to the morphology of a postsynaptic neuron, and keeping track of the synapse type and associated presynaptic cell type. Based on the presynaptic cell type of each synapse, ISf can generate spike times for each presynaptic source (see section Activity below). Assigning synapses onto the postsynaptic morphology is referred to as a ‘network embedding’. A network embedding for a given morphology is uniquely defined as a .syn and .con file.

ISF currently implements the following workflows to generate .syn and .con files:

• udvary2022

Activity¶

This section is responsible for generating activity patterns for the assigned synapses based in empirically observed PSTHs of the presynaptic neurons. ISF distinguishes two kinds of activity:

1. Ongoing activity: the baseline synaptic activity patterns in the absence of the in vivo condition of interest. The ongoing activity is defined in tandem with the network parameters in a Network parameters file.

2. Evoked activity: the activity patterns in response to a specific in vivo condition. Its file format is described in Activity data.

Modules¶