h1. Physiology & Morphology
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h1. Searching the Database

With the current launch of the Allen Cell Types Database, we include electrophysiological recordings from over 700 individual cells, a subset of which also include [morphological|#Morphology] reconstruction and [#Neuronal Models]. There are several methods to search this database; 1) enable specific [filter parameters|#Filters] by selecting from the "Filters" menu, 2) select a cell from the "[#Cell Location]" map, 3) use the slider bars in the [Parallel Coordinate Plot|#Parallel Coordinate Plot of the Cell Features] or 4) select from one of the curated [Electrophysiological or Morphological|#Curated Search] searches.

h2. Filters


!Filters.PNG|align=right,border=1,hspace=5,width=150!

To filter the neurons in your list of results, select from the [mouse line|#Mouse Lines], the cortical layer (1, 2/3, 4, 5, 6a, 6b), and the Cell Reporter (Positive or Negative). By {imagepopup:ImageName=Default.png}{*}default{*}{imagepopup}, only a subset of these cells are listed; however, you can alter the subset of cells represented by clicking on the "More Options+" link and selecting from categories that include "Hemisphere", "Dendrite Type", "Apical Dendrite", "Morphology", and "Models".

The [#Cell Location] viewer is integrated with the [#Parallel Coordinates Plot] and the Cell Summaries list of experimental results, and enables {imagepopup:ImageName=sortby.png}{*}sorting and coloring{*}{imagepopup} by the electrophysiological or morphological [features|#Cell Feature Filters]. Features to sort and color by include: Upstroke:Downstroke, Adaptation, Rheobase, Membrane Time Constant (Tau), Firing Rate, Input Resistance, Normalized Cortical Depth, Max Distance and # of Stems.

Clicking "Reset Filters" will return the settings to the default parameters.

h3. Mouse Lines

Whole-cell current clamp recordings were made from cells expressing the fluorescent molecule tdTomato (Reporter Positive) or from nearby non-fluorescent (Reporter Negative) cells. Fluorescent cells were Cre-positive cells from one of the transgenic lines described below. Whole-brain transgenic characterization of each Cre-line is available from the links below. To select a specific mouse line(s) click on the row(s) understanding that the layer refers to the selectivity of the fluorescence and "Type" refers to the putative Excitatory or Inhibitory cell type.

!MouseLines.png|border=1,align=left,hspace=10,width=250! *Cux2-CreERT2*\-Enriched in cortical layers 2/3/4, thalamus, midbrain, pons, medulla and cerebellum. View [transgenic characterization|http://connectivity.brain-map.org/projection/experiment/ivt?id=310439724,112777297,127175479,127175553,182530711,146454414,112607101,117260778,112606597,112603505,117285650,127171579,117277651,100144046&popup=true].
*Nr5a1-Cre*\-Expressed in restricted populations within the hypothalamus (ventromedial hypothalamus), and in cortical layer 4. View [transgenic characterization|http://connectivity.brain-map.org/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].
*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.brain-map.org/projection/experiment/ivt?id=263241470,81437122,81439484,81582731,80926425,81578090,81093825,81268764&popup=true].
*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.brain-map.org/projection/experiment/ivt?id=301583889,267224431,264031444,264031653,182020425,182020206,264031074,264033441,264033655,264030251,264030601&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.brain-map.org/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].
*Rbp4-Cre_KL100*\-Enriched in cortical layer 5 and the dentate gyrus. View [transgenic characterization|http://connectivity.brain-map.org/projection/experiment/ivt?id=166082128,127175265,167642756,180303012,127175627,146454705,146455572,146455334,127172728,127173967,117285137,117277436&popup=true].
*Ntsr1-Cre_GN220*\-Specific to cortical layer 6 neurons. View [transgenic characterization|http://connectivity.brain-map.org/projection/experiment/ivt?id=120584036,113103581,100147520,81747432,81582764,100141762,100141758,100132444,100132443,100141519,100134098,100134102,81709682,100142255,81578128&popup=true].
*Slc17a6-IRES-Cre*\-Widespread expression throughout most of the brain, except very sparse expression in the striatum and restricted populations within cerebellum, medulla, and pons. View [transgenic characterization|http://connectivity.brain-map.org/projection/experiment/ivt?id=266962653,304862407,100142487,100134091,100134093,100130502,100130503,100117977,100117972,100141518,100140890,100112816,308053545,308606176,100112813&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.brain-map.org/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].
*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.brain-map.org/projection/experiment/ivt?id=277800995,182530118,167643437,180310397,294350762,156350398,159123971,159120103,308604125,308052901,311809427,313182934&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.brain-map.org/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.brain-map.org/projection/experiment/ivt?id=167511639,100142491,100134108,100134111,100130475,100130474,100117967,100141535,100134107,100130479,100141727,308606913,100130499,308053761,100140886,100126201,313181852,311809644&popup=true].

h2. Cell Location

Cells were registered to the Allen Mouse Common Coordinate Framework (see whitepaper in "[celltypes:Documentation]") and are illustrated in the approximate location on the representation of the visual cortical areas (see image below). Cell locations in 2-D are represented in the center image view from a perspective above the brain and are annotated according to Wang and Burkhalter (J. Comp. Neurol., 502: 339--357. doi: 10.1002/cne.21286).

The cortical depth of the cell is indicated in either the coronal or the sagittal view, shown in the bottom and side views,  respectively. The coronal and sagittal views are labeled with the Pia (top of the brain), the White Matter (or bottom of the cortex) as well as the Lateral (L), Medial (M), Rostral (R) or Caudal (C) aspects of the brain.



!CellLocation.PNG|align=left,border=1!
|| B&W || AI || Structure Name ||
| V1 | VISp | Primary Visual Area |
| P | VISpl | Posterolateral visual area |
| POR | VISpor | Postrhinal area |
| LI | VISli | Laterointermediate area |
| LM | VISl | Lateral visual area |
| AL | VISal | Anterolateral visual area |
| RL | VISrl | Rostrolateral visual area |
| A | VISa | Anterior area |
| AM | VISam | Anteromedial visual area |
| PM | VISpm | Posteromedial visual area |
| n/a | RSPagl | Retrosplenial area, lateral agranular part |


Filtering the cells (using the [#Filters] parameters or the sliders in the [Parallel Coordinate Plot|#Parallel Coordinate Plot of the Cell Features]) will result in a decrease or increase in the number of cells visualized on this map.

Once you hover your mouse over a cell, the cell will be outlined in black and metadata for that cell will be displayed in the upper left hand corner of the map.


h2. Curated Search

Quick Electrophysiological or Morphological searches are available by clicking on those headings above the map.

h3. Morphological Curated Search

A fraction of the cells that were selected for imaging and reconstruction (see Morphology Overview whitepaper in [Documentation |celltypes:Documentation]for more details) showed enough morphological similarities that a curated search based on these features is available from the Morphology link above the Cell Location map. To find similar cells based on Normalized Cortical Depth and Mouse Line, click on the average morphology thumbnail to pull up a list of cells that fit that criteria. Note: the number of cells that fit the criteria is listed in the title banner of the Filters box.

!MorphologySearch.PNG|border=1!

h3. Electrophysiological Curated Search

A fraction of cells with well-characterized electrophysiological properties (see Electrophysiology Overview whitepaper in [Documentation |celltypes:Documentation]for more details) have been selected for a curated search and are available by clicking on the Electrophysiology link from above the Cell Location map. These searches select for cell types with regular to moderate to fast spiking rates with unique adaptation or time constant parameters. To select the cells with these characteristics, click on the image. Note: the number of cells that fit the criteria is listed in the title banner of the Filters box.


!EphysSearch.PNG|border=1!

h2. Parallel Coordinate Plot of the Cell Features

Another way to visualize this data, which has many distinct and sometimes unrelated dimensions, is a Parallel Coordinate Plot. This visualization plots each cell according to a finite number of electrophysiological and/or morphological features.

!ParallelCoord.PNG|border=1!


!Mode.PNG|align=right,border=1,hspace=5! When you have selected the Electrophysiology Mode from the Filters box, six features are illustrated in the Parallel Coordinate Plot: Upstroke/Downstroke Ratio, Adaptation Index, Rheobase, Membrane Time Constant (Tau) and Input Resistance. When the "Electrophysiology + Morphology" mode is instead selected, again six features are shown: three electrophysiology features; Upstroke/Downstroke Ratio, Adaptation Index and Rheobase, as well as three Morphology features: Normalized Cortical Depth, Max Distance and # Stems.

You can limit your search by using the slider bars on each axis. Hovering your mouse over the axis of the parameter you are interested in inspecting will illuminate the data included in your search. Click and drag from the extremes of the axis to limit your search.


!Sliders.PNG|border=1!


Each of the axes can be relocated by clicking and dragging the title to another position along the x-axis.

h2. Electrophysiology Features


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 Overview whitepaper in the "[celltypes:Documentation]" tab and/or [download the data|celltypes:API] from the Allen Brain Atlas API. These features were selected not only by what they were able to tell us about the intrinsic properties of the cells, but also in their ability to differentiate between putative cell types in a non-biased clustering analysis.

!UpstrokeDownstroke.JPG|border=1!

h5. 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 illustrated here.

This parameter is used to distinguish between spiny (putatively excitatory) and aspiny (putatively inhibitory) groups of cells in a non-biased clustering analysis.


h5. Adaptation Index

Not only are isolated action potentials of interest, but the rates of firing are likely to be important in inter-neuron communication. The adaptation index is the rate at which action potential firing changes during a stimulus. This index is used to characterize a neurons response to a sustained input, a one second square pulse in this case.

A high adaptation index means the neuron spikes at the beginning of the stimulus, but then the spiking slows or stops altogether. These neurons therefore are likely transmit the initiation of an upstream input. Conversely, a neuron that does not accommodate (has a low Adaptation index) gives a consistent output during the sustained input and might also be used to tell when a stimulus ends. The adaptation index likely involves ion channel proteins that change properties on the time scale of hundreds of milliseconds to seconds.

h5. Rheobase

This value is the amount of stimulus current (long square current in pA) required to initiate a single action potential. This parameter gives us an indication of the excitability and the membrane resistance of the cell.

h5. Membrane Time Constant


!TauEstimation.PNG|align=right,border=1,hspace=5,width=300! The membrane time constant, also referred to as tau, reflects the time it takes for a neuron to charge its membrane. This is one of the passive or subthreshold properties of the cell and is the product of the [input resistance|#Input Resistance] and the cell capacitance. The membrane time constant in this study was estimated by fitting voltage responses to negative current injection with an exponential.

h5. Firing Rate


!FiringRate.PNG|align=right,border=1,hspace=10,width=500! The firing rate is simply the speed at which a neuron fires multiple action potentials in sequence given a sustained current injection. A neuron that fires at a faster rate could influence a downstream neuron more strongly than a neuron firing with a slower rate. The rate that a neuron fires given a sustained input is determined by the ion channel proteins it expresses and whether and how fast those ion channel proteins recover from the previous action potential. In general, a higher firing rate is seen in neurons with individual action potentials that are more narrow and have a deeper after hyperpolarization. This is illustrated in the [parallel coordinate plot|#Parallel Coordinates Plot] where cells with a greater Upstroke/Downstroke ratio show a lower firing rate.

h5. Input Resistance


!VIplot.PNG|align=right,thumbnail,border=1,hspace=5! The input resistance is the baseline resistance of the neuron membrane, and like [tau|#Membrane Time Constant] is one of the passive or subthreshold properties of the cell. A cell with high input resistance leads to a large voltage response (V=IR) and is referred to as "tight" as current doesn't easily leak out. Conversely "leaky" neurons are those with low input resistance. The input resistance was calculated by measuring the slope of the V/I plot at subthreshold potentials.
\\

h2. Morphology Features

A subset of cells with electrophysiological recordings was manually selected to enter our 3-D reconstruction pipeline. Similar to the electrophysiology features, many morphology features were calculated in the reconstruction, but only three are called out in the web application; Normalized Cortical Depth, Max Distance and # Stems. To see the entire array of morphological features, please read the Morphology Overview whitepaper in "[celltypes:Documentation]" or [download the data|celltypes:API] from the Allen Brain Atlas API.

The three features represented in the web application were the top three most discriminative features (ranked by a classic machine learning technique) that best separates major morphological categories of neurons currently included in the database.

h5. Normalized Cortical Depth

As the thickness of the visual cortex changes naturally and can also be affected by non-biological factors like tissue shrinkage during histology, we compute the relative depth of the soma with respect to the pia and white matter using the cortical coordinate space in the CCF (see whitepaper in [celltypes:Documentation]).

h5. Maximum Distance

This is the maximum {imagepopup:ImageName=eucdistance.jpg}{*}Euclidean distance{*}{imagepopup} of all the nodes. Euclidean distance is the straight line distance from the soma (root) to the node. The maximum euclidean distance is able to distinguish a particular category of spiny neuron ("tall, tufted") from a particular category of aspiny neuron ("common type").

h5. Number of Stems

The {imagepopup:ImageName=Stems.jpg}{*}number of stems{*}{imagepopup} attached to the soma. The # Stems is used to distinguish between two categories of spiny neurons (“star pyramid” versus “tufted”).

h1. Electrophysiology Results

Filtering of the dataset results in a list of experiments ranked (by default) by Upstroke:Downstroke. You can alter the sort parameters from the [#Filters] menu.


!CellSummaries.PNG|border=1!



!AP.PNG|align=right,border=1,hspace=5! Each experiment lists metadata regarding the classification of the cell, including the Cre-line, the Area, the Layer, Cell Reporter (positive or negative), the Dendrite Type as well as whether or not the Apical Dendrite is intact. It also includes thumbnails showing the electrical traces, a trace of the action potential from which many of the electrophysiological [features|#Electrophysiology Features] are calculated and (when available) the reconstructed neuron.

If you have selected several cells to compare, you can save this or other kinds of searches by selecting the "Permalink" feature.

Clicking anywhere in a cell's results box will open a new page with the experimental details.

h2. Experimental Detail Page - Electrophysiology

The Experimental Detail page includes the Electrophysiological Summary and a workspace to Browse Electrophysiology Data. The Electrophysiology Summary includes a thumbnail of the location of the cell mapped to the CCF, metadata on the cell including Mouse Line, ID, Area, Cell Reporter, Dendrite Type, Apical Dendrite and hemisphere. Values from each of the electrophysiology [cell features|#Cell Feature Filters] are also listed along with model parameters (where appropriate). You can also view plots of the F/I and V/I curves here.

Clicking on the image of the cell (when available) will open a new page containing the [#Morphology] data.

!EphysSummary.PNG|border=1!


The electrophysiological data itself can be viewed from this page, or [downloaded|celltypes:Download] to be visualized on another platform or in a third party program. The Allen SDK provides a simple Python module to support downloading metadata and NWB files for cells in the Allen Cell Types Database.  Please see the [Data API Client|http://alleninstitute.github.io/AllenSDK/cell_types.html] documentation page to see an example.



!Browse.JPG|border=1!

# *Select Stimulus type*: A drop-down menu from which you can select the [stimulus type|#Stimulus Types] and see the resulting Cell Response.
# *Select Neuronal Model*: When available, [neuronal models|#Neuronal Models] have been run on the data and when selected will open below the recorded Cell Response.
# *Download Data*: This link will download the .nwb file with the data from this experiment. For more information, please see [here|celltypes:API].
# *Select Sweep*: Select sweeps will be available for you to inspect from this view. As you hover your mouse over each colored square, not only do you see the resulting graphs change to reflect the sweep selected, but you also will see sweep metadata (Sweep #, Stimulus amplitide (pA) and # of spikes) listed below the squares. Once you click on a colored square, you can use left/right arrow keys to move between the sweeps.
# *Slider Bar*: This feature allows you to zoom in and out of the Stimulus, Cell Response and Model views by clicking and dragging on the arrows.
# *Stimulus*: The stimulus injected into the cell.
# *Cell Response*: The response of the cell to the injected stimulus.
# *(Optional) Model Response*: When available, the model of the cellular response.

h5. 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

!StimTable.JPG!

!Stimulus.jpg|border=1!

h3. 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.{warning}

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 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.

More detailed information on each of the models is available in the whitepapers in [celltypes: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. |

h1. Morphology

When available: the Morphology page can be reached either by clicking on the image of the reconstructed cell in the search results page,

!SearchResultMorph.PNG|border=1!


or by clicking on the image of the cell on the Electrophysiological Detail Page.


!EphysSummary.JPG|border=1!

h2. Experimental Detail Page - Morphology

The Experimental Detail page includes the Morphology Summary and a workspace to Browse the Morphology Data. The Morphology Summary includes the location of the cell mapped to the CCF, metadata on the Mouse Line and location of the cell, as well as the Morphological features most appropriate to the data (see more information in the Morphology whitepaper in [celltypes:Documentation]).

Clicking on the image of the cell trace will open a new page containing the [#Electrophysiology Results] data.



!MorphSummary.PNG|border=1!


Projected views of the biocytin filled neuron were constructed by composing the darkest intensity pixel from each plane of the image stack into a single plane.

Projected top view and side view, as well as the 3-D neuron reconstruction can be viewed from this page


!MorphBrowse.PNG|border=1!



From the Projected top view, you can zoom into the picture from the on-screen navigation tools, the [#Keyboard Commands] or using your scroll wheel. The two views of the neuron are synched so zooming in on one will also zoom the other. Clicking on "View image stack" will take you to an [image viewer|#Morphology Image Stack] to view the individual images taken of this neuron.

The image viewer of the 3-D neuron reconstruction allows for visualization of the reconstructed neuron using the onscreen navigation tools. Clicking "Reset" will reset the neuron to its default view. The legend in the 3D reconstruction indicates the various components of the reconstruction.

You can download both the reconstruction (as an .swc file) or the calculated morphological measurements (as an XML) from the links below the viewers. For more information please see the [API Documentation|celltypes:API].

h5. Morphology Image Stack

Clicking "View Image Stack" while browsing the Morphology data will take you to our image viewer. The title bar includes the Mouse Line, the Specimen ID, the structure and the hemisphere.  The "Configure" icon opens a menu that will allow you to vary the image contrast and download the individual images. The entire image stack can be navigated through using the on screen navigation tools, using the [#Keyboard Commands] or by clicking on the Projected Side View.

!MorphZAP.JPG|border=1,width=800!


h5. Scale Bar

Shows the current viewing resolution of the image, in microns. This  value dynamically changes as you zoom in/out of the image. You can  position the scale bar anywhere on the main image by dragging the scale  bar by its ruler.


!help_hscalebar.png! !help_vscalebar.png!

You can toggle the orientation of the scale bar from horizontal to vertical by clicking on the scale bar text.

h5. Keyboard Commands

|| *Key* || *Description* ||
| 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 |