Cell Types Data
Searching the Database
With the initial launch of the Allen Cell Types Database, we include electrophysiological recordings from 248 individual cells,
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Mouse Lines
Rorb-IRES2-Cre-Strong expression in the zonal layer of the superior colliculus and subregions of thalamus. Dense, patchy expression in layer 4 and sparse expression in layer 5 and 6 in cortex. Also expressed in trigeminal nucleus and small patches of cells in cerebellum. View transgenic characterization.
Scnn1a-Tg2-Cre-Reporter expression in sparse and/or restricted regions of cortex (layer 4), thalamus, midbrain, medulla, pons, and cerebellum. View transgenic characterization.
Scnn1a-Tg3-Cre-Enriched in cortical layer 4 and in restricted populations within cortex, thalamus, and in cerebellum. View transgenic characterization.
Nr5a1-Cre-
Rbp4-Cre_KL100-
Ntsr1-Cre-
Sst-IRES-Cre-
Pvalb-IRES-Cre-
Htr3a-Cre_NO152-
Gad2-IRES-Cre-
Cell Feature Filters
Stimulus Types
ELECTROPHYSIOLOGY STIMULI STRATEGY AND DETAILS
Different sets of stimulation waveforms were used in order to:
- Interrogate intrinsic membrane mechanisms that underlie the input/output function of neurons
- Linear and non-linear subthreshold properties
- Action potential initiation and propagation
- Afterhyperpolarization/afterdepolarization
- Understand aspects of neural response properties in vivo
- Stimulation frequency dependence (theta vs. gamma) of spike initiation mechanisms
- Ion channel states due to different resting potentials in vivo
- Construct and test computational models of varying complexity emulating the neural response to stereotyped stimuli
- Generalized leaky-integrate-and-fire (GLIF) models
- 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 |
Description |
|---|---|
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. |
Biophysical-Perisomatic |
Models with active conductances at the soma and passive dendritic morphology based on full 3D reconstruction. |