Cell Types Data

Searching the Database

With the initial launch of the Allen Cell Types Database, we include electrophysiological recordings from 248 individual cells,


Mouse Lines

Cell Feature Filters

Stimulus Types


Different sets of stimulation waveforms were used in order to:

  1. Interrogate intrinsic membrane mechanisms that underlie the input/output function of neurons
    1. Linear and non-linear subthreshold properties
    2. Action potential initiation and propagation
    3. Afterhyperpolarization/afterdepolarization
  2. Understand aspects of neural response properties in vivo
    1. Stimulation frequency dependence (theta vs. gamma) of spike initiation mechanisms
    2. Ion channel states due to different resting potentials in vivo
  3. Construct and test computational models of varying complexity emulating the neural response to stereotyped stimuli
    1. Generalized leaky-integrate-and-fire (GLIF) models
    2. Biophysically and morphologically realistic conductance-based compartmental models

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 are simple point neuron models which represent the neuron as a single compartment.

There are five levels of GLIF models with increasing 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


1. Leaky Integrate and Fire (LIF)

Standard circuit representation of a resistor and capacitor in parallel with a leaky membrane.

2. LIF + Reset Rules (LIF-R)

LIF with biologically-derived threshold and voltage reset rules in addition to a biologically derived threshold decay.

3. LIF + Afterspike Currents (LIF-ASC)

LIF with spike-induced currents to model long-term effects of voltage-activated ion channels.

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

LIF with additional Reset Rules and Afterspike Currents.

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

All of the above, with an additional voltage-dependent component of threshold.


Models with active conductances at the soma and passive dendritic morphology based on full 3D reconstruction.

Generalized Leaky-Integrate-and-Fire (GLIF) Models

Biophysical Models - Perisomatic