h1. Cell Types Data

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h2. Searching the Database

With the initial launch of the Allen Cell Types Database, we include electrophysiological recordings from 248 individual cells, a sub-set of which also include [morphological|#Morphology] reconstruction and [#Neuronal Models]. To search this database, enable specific [filter parameters|#Filters] by selecting from the "Filters" menu. By {imagepopup:ImageName=DefaultListing.jpg}default{imagepopup} 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".


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h3. Filters

To filter the neurons in your list of results select from the [mouse line|#Mouse Lines], the cortical [layer|#Layers], and the hemisphere (left, right or either). You can {imagepopup:ImageName=Sortby.jpg}sort{imagepopup} the results by the electrophysiological or morphological [features|#Cell Feature Filters].

h4. 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. 

!FilterMouseLine.JPG|border=1,align=left,hspace=10!  *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|http://connectivity/projection/experiment/ivt?id=301583889,267224431,264031444,264031653,182020425,182020206,264031074,264033441,264033655,264030251,264030601&popup=true].
*Scnn1a-Tg2-Cre*-Reporter expression in sparse and/or restricted regions of cortex (layer 4), thalamus, midbrain, medulla, pons, and cerebellum. View [transgenic characterization|http://connectivity/projection/experiment/ivt?id=263241470,81437122,81439484,81582731,80926425,81578090,81093825,81268764&popup=true].
*Scnn1a-Tg3-Cre*-Enriched in cortical layer 4 and in restricted populations within cortex, thalamus, and in cerebellum. View [transgenic characterization|http://connectivity/projection/experiment/ivt?id=183374804,180301742,180301668,156347914,81747435,81582728,81657993,146453657,146453730,127171291,127170789,146453583,81709690,100142254,81448973,81093827,81578088,112199140,112199214&popup=true].
*Nr5a1-Cre*-Expressed in restricted populations within the hypothalamus (ventromedial hypothalamus), and in cortical layer 4. View [transgenic characterization|http://connectivity/projection/experiment/ivt?id=265929196,180300351,180304278,180302247,100146209,180301816,100138023,100138110,100132446,100132445,100138602,100140741,100141521,182677985,100140743,304700386,304700172,182682473,182682547,100134122,182682697,100140619,182677483,304701028,304700600,304700814,311808558,311808992,313181420,313181636&popup=true].
*Rbp4-Cre_KL100*-Enriched in cortical layer 5 and the dentate gyrus. View [transgenic characterization|http://connectivity/projection/experiment/ivt?id=166082128,127175265,167642756,180303012,127175627,146454705,146455572,146455334,127172728,127173967,117285137,117277436&popup=true].
*Ntsr1-Cre*-Specific to cortical layer 6 neurons. View [transgenic characterization|http://connectivity/projection/experiment/ivt?id=120584036,113103581,100147520,81747432,81582764,100141762,100141758,100132444,100132443,100141519,100134098,100134102,81709682,100142255,81578128&popup=true].
*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|http://connectivity/projection/experiment/ivt?id=277800995,182530118,167643437,180310397,294350762,156350398,159123971,159120103,308604125,308052901,311809427,313182934&popup=true].
*Pvalb-IRES-Cre*-Expressed in restricted and/or sparse populations within the cerebellum, medulla, pons, midbrain, cortex, hippocampus, thalamus, and striatum. View [transgenic characterization|http://connectivity/projection/experiment/ivt?id=166562678,111192541,81747438,81657975,81747441,81657984,100134103,100130498,100130508,100117968,100117976,100141217,100141536,81658021,81721696,81721692,81709692,100144576,100144585,100144587,100144584&popup=true].
*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|http://connectivity/projection/experiment/ivt?id=305489377,309712164,308053975,308054194,308607812,308608605&popup=true].
*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|http://connectivity/projection/experiment/ivt?id=167511639,100142491,100134108,100134111,100130475,100130474,100117967,100141535,100134107,100130479,100141727,308606913,100130499,308053761,100140886,100126201,313181852,311809644&popup=true].

h4. Layer

Search results can be filtered by cortical layer by selecting one or more layers from the drop-down menu. 
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h3. Cell Feature Filters

While many distinct electrophysiological features were recorded and/or calculated from each cell, only a few features were called out in the web application. To see the other features, please read the Electrophysiology whitepaper in the "[celltypes:Documentation]" tab and/or [download the data|celltypes:API] from the Allen SDK.

When you have selected the "{imagepopup:ImageName=EphysFeatures.jpg}Electrophysiology{imagepopup}" Mode, six features are illustrated in the [#Parallel Coordinate Plot]: Upstroke/Downstroke Ratio, Fast AP Trough, FI Curve Slope, Rheobase, Ramp AP Time and Resting Vm. When the "{imagepopup:ImageName=MorphFeat.jpg}Electrophysiology + Morphology{imagepopup}" Mode is selected, again only six features are shown: four electrophysiology features; Upstroke/Downstroke Ratio, FI Curve Slope, Rheobase and Resting Vm, as well as two Morphology features: Max Distance and # Stems.

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h4. Upstroke/Downstroke Ratio

!highvslowratio.jpg|align=right,border=1! The ratio between the absolute values of the action potential peak upstroke and the action potential peak downstroke. _Action potential peak upstroke:_ The maximum rate of change between the action potential threshold and the action potential peak. _Action potential peak downstroke:_ The minimum rate of change between the action potential peak and the action potential trough.

This value gives us an indication of the amount of time a cell takes to recover after an Action Potential. An example of the difference between a high and a low ratio is demonstrated here.


h4. Fast AP Trough

Minimum value of the membrane potential in the interval lasting 5 ms after the peak.

h4. FI Curve SlopeThis value gives us an indication of the kinds of ion channels that are present in a cell. {color:red}*[JB - how is this different from an after hyperpolerization]*{color}

h4. FI Curve Slope

While some of the features probe the firing patterns of single action potentials, we also calculated features based on multiple sweeps of the cell. The F/I Curve Slope calculates the number of action potentials per unit of current injection and probes the excitability and the firing pattern of a cell.


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h4. Rheobase

h4. Ramp AP Time

h4. Resting Vm




h3. Stimulus Types

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

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h2. Electrophysiology

h3. 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. |



h4. Generalized Leaky-Integrate-and-Fire (GLIF) Models

h4. Biophysical Models - Perisomatic

h2. Morphology