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- 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
| Warning |
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Reprocessing of the data occurred for the March 2016 release so any analysis performed prior to the March 2016 release date should be performed again with the new models. |
The Allen Cell Types Database contains three types of neuronal models: two 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 biophysical models take into account dendritic morphological structure, whereas GLIF models are simple point neuron models that 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.
For more detailed information on each of the models, see the Documentation.
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Model Name
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Description
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1. Leaky Integrate and Fire (LIF)
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Standard circuit representation of a resistor and capacitor in parallel with a leaky membrane.
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2. LIF + Reset Rules (LIF-R)
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LIF with biologically-derived threshold and voltage reset rules in addition to a biologically derived threshold decay.
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3. LIF + Afterspike Currents (LIF-ASC)
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LIF with spike-induced currents to model long-term effects of voltage-activated ion channels.
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4. LIF-R + Afterspike Currents (LIF-R-ASC)
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LIF with additional Reset Rules and Afterspike Currents.
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5. LIF-R-ASC + Threshold Adaptation (LIF-R-ASC-A)
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All of the above, with an additional voltage-dependent component of threshold.
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Biophysical-Perisomatic
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Biophysically realistic, single-neuron model with passive dendrites and active soma.
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Biophysical-All Active
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Biophysically realistic, single-neuron model with active conductances everywhere.
Morphology details page
The morphology details page gives you access to the available morphological information for a given cell. The top section of the page provides a summary of the cell properties, while the second allows you view projections of the biocytin filled neuron on two orthogonal planes and the neuron's 3D morphology reconstruction. You can also view the stack of high resolution images used for the reconstruction. For details on the imaging and neuron reconstruction methods, see the Documentation.
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Key | Description |
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F | Advance to the next image from the specimen |
D | Go back to the previous image from the specimen |
A | Zoom in |
Z | Zoom out |
Neuronal Models
| Warning |
|---|
Reprocessing of the data occurred for the March 2016 release so any analysis performed prior to the March 2016 release date should be performed again with the new models. |
The Allen Cell Types Database contains three types of neuronal models: two 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 biophysical models take into account dendritic morphological structure, whereas GLIF models are simple point neuron models that 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.
For more detailed information on each of the models, see the Documentation.
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 | Biophysically realistic, single-neuron model with passive dendrites and active soma. |
Biophysical-All Active | Biophysically realistic, single-neuron model with active conductances everywhere. |
Data access and download
As inidicated above, you can download electrophysiology recordings, morphology image data, 3D reconstructions and neuronal model parameters using links in the electrophysiology and morphology details pages for a cell.
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