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Single Cell Neuronal Models

The Allen Cell Types Database contains two types of neuronal models: perisomatic biophysical models and generalized leaky integrate-and-fire (GLIF) models.  These models attempt to mathematically reproduce a cell's recorded response to a current injection.  The perisomatic biophysical models take into account dendritic morphological structure, whereas GLIF models rely strictly on the cell's stimulus and response. 

There are five types of GLIF models with varying levels of complexity.  The most basic model is a simple leaky integrate-and-fire equation.  More advanced GLIFs attempt to model variable spike threshold, afterspike currents, and threshold adaptation. 

Model Name


Biophysical, perisomatic


1 Leak Integrate and Fire (LIF)


2 LIF + Reset Rules (LIF-R)


3 LIF + Afterspike Currents (LIF-ASC)


4 LIF-R + Afterspike Currents (LIF-R-ASC)


5 LIF-R-ASC + Threshold Adaptation (LIF-R-ASC-A)


Please see the perisomatic biophysical and GLIF technical white papers for more details on how these models were created (TODO). Image Added
A cell's electrophysiology page displays all available models.  Choose a model to see its simulated response to all stimuli presented to the cell.  If the required sweeps are available, two model evaluation metrics are computed per model:

Metric Name

Required Sweeps


Explained Variance Ratio

Noise 2 (at least two)


Feature Average

Sweeps used for biophysical model fitting


* rheobase is defined as the Long Square amplitude

All models in the Allen Cell Types Database are available for download and local execution via theAllen Software Development Kit (SDK).  The biophysical models require NEURON to be run, which the SDK helps to configure.  The GLIF simulation module comes as part of the Allen SDK. 

To download all of the configuration files necessary to run model 472427473:

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