Cell Types Data

Searching the Database

With the initial launch of the Allen Cell Types Database, we include electrophysiological recordings from 248 individual cells, of which a portion of those cells also include morphological reconstruction and [#Neuronal Models]. To search this database, enable specific [filter parameters] by selecting from the "Filters" menu. By

only a sub-set of these cells are listed; however, you can alter the sub-set of cells represented by clicking on the "More Options+" link and selecting from categories that include "Dendrite Type", "Morphology", "Models" and "Apical Dendrite".

Electrophysiology

Filters

To filter the neurons in your list of results select from the [mouse line], the cortical [layer], and the hemisphere (left, right or either). You can

the results by the electrophysiological or morphological features.

Mouse Lines

Whole cell current clamp recordings were made from cells expressing the fluorescent molecule, tdTomato. Fluorescent cells were cre-positive cells from one of the transgenic lines described below.

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-Expressed in restricted populations within the hypothalamus (ventromedial hypothalamus), and in cortical layer 4. View transgenic characterization.
Rbp4-Cre_KL100-Enriched in cortical layer 5 and the dentate gyrus. View transgenic characterization.
Ntsr1-Cre-Specific to cortical layer 6 neurons. View transgenic characterization.
Sst-IRES-Cre-Strong scattered expression throughout the brain. Localized areas of enrichment include restricted populations in thalamus, amygdala, midbrain, hindbrain, cortical subplate, and Purkinje cell layer. View transgenic characterization.
Pvalb-IRES-Cre-Expressed in restricted and/or sparse populations within the cerebellum, medulla, pons, midbrain, cortex, hippocampus, thalamus, and striatum. View transgenic characterization.
Htr3a-Cre_NO152-Reporter expression is detected in a subset of cortical interneurons. Enrichment is also detected in restricted populations within olfactory areas, pallidum, hypothalamus, pons, medulla, and cerebellum. View transgenic characterization.
Gad2-IRES-Cre-Specific to GABAergic neurons. Enriched in the striatum, piriform cortex, and within restricted populations in the thalamus, hypothalamus, cerebellum, olfactory areas, and GABAergic interneurons of the cortex. View transgenic characterization.

Layer

Search results can be filtered by cortical layer by selecting one or more layers from the drop-down menu.

Cell Feature Filters

Upstroke/Downstroke Ratio

The ratio between the absolute values of the action potential peak upstroke and the action potential peak downstroke.

Stimulus Types

ELECTROPHYSIOLOGY STIMULI STRATEGY AND DETAILS

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. 

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

Biophysical Models - Perisomatic

Morphology