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h1. Cell Types Data


h1. 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|#Filters] by selecting from the 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".


h2. Electrophysiology

h2h3. Filters

To filter the neurons in your list 

h3of results select from the [mouse line|#Mouse Lines], the cortical [layer|#Layers], and the hemisphere (left, right or either). You can sort the results by the 

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].

h3h4. Layer

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

h2h3. Cell Feature Filters

h2h3. 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



h2h3. 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. |

h3. Generalized Leaky-Integrate-and-Fire (GLIF) Models

h3. Biophysical Models - Perisomatic

h2. Morphology