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h1. Electrophysiology and 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 sub-set 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) selecting 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 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 "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-florescent (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 florescence 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: VISp - primary visual area, VISpl - visual area posterolateral, VISpor - [?], VISli - [?], VISl - visual area lateral, VISal - visual area anterolateral, VISrl - [?], VISa - visual area [?], VISam - visual area anteromedial, VISpm - visual area posteromedial and RSPagl - retrosplenial area, lateral agranular part. The cortical depth of the cell is indicated in either the coronal or the saggital view, shown in the bottom and side views,  respectively. The coronal and saggital 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|border=1!


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 meta-data 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 dropdown 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.

!MorphologySearch.PNG|border=1!


h2. Parallel Coordinate Plot of the Cell Features

To be able to visualize this data, which has many distinct and sometimes unrelated dimensions, we used a Parallel Coordinate Plot. This visualization plots each cell according to 6 electrophysiological or morphological features.
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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.

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.

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!Sliders.JPG|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 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.


{color:red}Features have changed, will need updating{color}

!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 demonstrated 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. Fast AP Trough

Minimum value of the membrane potential in the interval lasting 5 ms after the peak of the initial action potential. Notice in the example above of a High vs. Low ratio, the Fast AP Trough values are related.

This value gives us an indication of the kinds of potassium ion channels that are present in a cell and can be an indication of how fast the neuron can recover after an action potential. This value helps contribute to separating spiny and aspiny cells when used in combination with upstroke:downstroke.

h5. FI Curve Slope


!FICurveSlope.JPG|border=1,align=right,hspace=5! While some of the features we have represented in the application probe the firing patterns of single action potentials, we also calculated features based on multiple successive sweeps recorded from the cell. The F/I Curve Slope is the slope calculated in the dynamic range of action potential firing as a function of the current injected into the cell (in pA). This value indicates the excitability and the bandwidth of a cell.

This value was instrumental in distinguishing among the aspiny cells (i.e. it clustered the fast-spiking Pvalb cells)

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. Ramp AP Time

This value is the time required to initiate a single action potential by a steady ramp of current injection (25 pA/sec). This value, while similar to Rheobase, was collected in a different manner that can reveal slower processes in a cell that can affect its firing. In an unbiased cluster analysis of cell types this parameter was one of the best parameters for differentiating among spiny neurons.

h5. Resting Vm

The resting membrane potential was measured soon after breaking into the cell and measures the membrane potential of a neuron at rest with no applied current.

h2. Morphology Features

A sub-set 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 two are called out in the web application; Max Distance and # Stems. To see the entire array of morphological features, please read the whitepaper in "[celltypes:Documentation]" or [download the data|celltypes:API] from the Allen Brain Atlas API.

The two features represented in the web application were the top two most discriminative features (ranked by a classic machine learning technique) that best separates major morphological categories of neurons currently included in the database. “Max Euclidean Distance” is able to distinguish a particular category of spiny neuron ("tall, tufted") from a particular category of aspiny neuron ("common type").  While “# Stems” can distinguish between two categories of spiny neurons (“star pyramid” versus “tufted”). These morphology categories are some of the most common in this dataset.

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.

h5. Number of Stems

The {imagepopup:ImageName=Stems.jpg}number of stems{imagepopup} attached to the soma.

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.

!ResultsList.JPG|border=1!

Each experiment lists meta-data regarding the classification of the cell, including the Cre-line, the location (hemisphere, layer and area) as well as annotation of the dendrites. It also includes six cell feature values depending upon whether you are looking only at electrophysiological data or if you have selected both electrophysiological and morphological data.

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 the Electrophysiology Data. The Electrophysiology Summary includes images of the cell and the location of the cell mapped to the CCF, meta-data on the Mouse Line and location of the cell, as well as the [cell features|#Cell Feature Filters] most appropriate to the search parameters. It also includes model fit parameters (where appropriate). You can also view plots of the F/I and V/I curves here.

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


!EphysSummary.JPG|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 meta-data (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

{color:red}The data since the 2015 release has been re-processed, so if you used the models last year, run it again with the new ones.{color}

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. 

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* \\ | Models with active conductances at the soma and passive dendritic morphology based on full 3-D reconstruction. |

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,

!Morph1.JPG|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, meta-data 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.


!MorphSumm.JPG|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.JPG|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 "Front" will reset the neuron to it's default view.

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 location from which the cell came as well as 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!


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 |