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h1. Neuronal Response: Two-Photon Calcium Imaging
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The first data modality to be released from the Allen Brain Observatory is a standardized _in vivo_ survey of physiological activity in the mouse visual cortex, featuring representations of visually evoked calcium responses from GCaMP6-expressing neurons at selected cortical depths, visual areas and Cre lines. 

h2. Searching the Data

From the landing page, you can searchexplore forthe cell responses by clicking on 1) the cre-transgenic mouse line, 2) the visualcortical area orand 3) the cortical depth of each of the experiments conducted in this surveystudy. 

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The current release includes a variety of data visualization summaries capturing visual coding properties of single cell and cell population responses to visual stimuli. Detailed information regarding each of the visual stimuli is available by clicking on the stimulus from the panel below the cortical imaging locations.


!VisualStimuliPanel.PNG|width=500px!


This resource introduces new visualizations that summarize the cellular responses for each visual stimulus in a single figure:


!thumbnails.png!

Further details on how to interpret each visualizations and how they were created is also available by clicking on the individual "Visual Stimuli" thumbnails below the cortical imaging locations.

Access to a list of experiments and the population responses for each experiment is available by clicking on the "Experiments" tab in the menu banner.  

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h2. Experiment Overview

!VisualAreas.PNG|align=right,border=1,hspace=5,width=250px! In this study, an experiment is composed of a series of three one-hour long two-photon calcium imaging sessions on an awake mouse exposed to a series of visual stimuli.  An experiment is the unique combination of one mouse, one imaging depth (e.g. 175 um from surface of cortex), and one visual area (e.g. “Anterolateral visual area” or “VISal”).  More information on the experimental design and the visual stimuli can be found from the whitepapers located in [observatory:Documentation].

h3. Targeted Functional Visual Areas

|| Area\*|| Abbreviation ||Structure Name||
| V1| VISp| Primary visual area|
| LM| VISl| Lateral visual area|
| AL| VISal| Anterolateral visual area|
| PM| VISpm| Posteromedial visual area|
\*Wang and Burkhalter (J.Comp.Neurol., 502: 339-357. doi: 10.1002/cne.21286)

h3. Transgenic Lines 

Two-photon calcium imaging was recorded in neurons expressing a calcium sensitive fluorescent molecule. This is made possible by the use of animals harboring a genetically encoded calcium sensor, GCaMP6, which is imparted by use of the Ai93 line and expressed in subsets of cell populations due to a combinatorial transgenic line breeding strategy. The transgenic lines are a cross of CaMK2a-tTA - a transgene directing tetracycline-controlled transactivator protein (tTA) expression in forebrain excitatory neurons - and one of the following:

* Cux2-CreERT2
* Rorb-IRES2-Cre
* Rbp4-Cre_KL100
* Nr5a1-Cre
* Scnn1a-Tg3-Cre
* Emx1-IRES-Cre

Florescent characterization of each of these triple transgenic mouse lines is available by clicking on the Transgenic Characterization tab in the menu banner. Further characterization of each of these transgenic lines can be found in the Transgenic Mouse Catalog in [observatory:Documentation].

h2. Searching from the Experiment Overview Page

Each experiment in the study is displayed as a row in the Experiment overview page. The columns that uniquely describe an experiment and can be used to sort the data are the "Area", "Driver 1" and "Imaging Depth".  The experiments are sorted by the first column and the columns can be moved by clicking and dragging on the column header. 


!CorticalMaptoRow.png|border=1!


!Columns.PNG|align=right,border=1,hspace=5,width=150px! With the inaugural release, all of the columns (minus the two common mouse lines) are displayed by default. Clicking on a row in the "View Cells" or "Experiment" columns will take you to the respective [#Cell List] or [#Experiment Detail Page]. Each of the remaining columns displays a visualization summarizing the population response of the neurons in the imaging field of view to the specific visual stimuli. The population thumbnails are shown below and can be explored in more detail from the [#Experiment Detail Page].


!PopulationThumbnails.png|border=1!


!StimulusColorGraph.PNG|border=1,align=right,width=200px,hspace=5! The population thumbnails are segregated by visual stimulus as indicated by the stimulus color key.


h2. Experiment Detail Page

The experiment detail page presents a more detailed view of all the information for a single experiment.  Each experiment is composed of three approximately one-hour imaging sessions. 

h3. Imaging Experimental Design

!StimulusDesign.png|width=600px!

For more information on the visual stimulus set, see the Stimulus Set and Response Analysis whitepaper in [observatory:Documentation].

h3. Experimental Metadata and Summary Images

Metadata for the experiment is listed at the top of the page including transgenic lines, targeted functional visual areas, imaging depth as well as a link to the [#Cell List], which identifies each responding cell in the two-photon calcium imaging sessions. Summary images taken from each of the imaging sessions are included under the metadata.

!ExperimentDetail.PNG!
!CorticalFOV.PNG!

h3. Population Thumbnails

Below the summary images and metadata are large versions of each of the population thumbnails shown on the [#Experiment Overview] page, with a description of what the thumbnail represents.

||*Visual Stimulus*||*Thumbnail*||*Description*||
| *Drifting Gratings*| Preferred Direction| Population summary of preferred drift direction of responsive cells|
| | Orientation Selectivity| Cumulative histogram plot indicating the population selectivity for orientation|
| | Direction Selectivity| Cumulative histogram plot indicating the population selectivity for direction|
| | Preferred Temporal Frequency| Histogram plotting the number of cells vs. the temporal frequency (Hz)|
| *Static Grating*| Preferred Orientation| Population summary of the preferred orientation of the responding cells|
| | Preferred Spatial Frequency| Histogram plotting the number of cells vs. the spatial frequency (cycles/deg)|
| | Orientation Selectivity| Cumulative histogram plot indicating the population selectivity for orientation|
| | Time to Peak| Temporal dynamics of the mean response time of the responsive cells|
| *Natural Scene*| Time to Peak| Temporal dynamics of the mean response time of the responsive cells|

h2. Cell List

This page lists all the relevant cells from the selected experiment and shows the cellular responses at a deeper level. Each row represents a single cell and illustrates the cell response through a series of thumbnails that represent a summary of the cellular response to a visual stimuli. Clicking on a row will take you to the [#Cell Detail Page].


!thumbnails.png!

More information on the development of each of the thumbnails and it's corresponding visual stimulus can be found from the "Visual Stimuli" buttons on the [Overview |http://observatory.brain-map.org/visualcoding]page.

h3. Filtering Cells

To explore the cellular responses within a single experiment, first click on the "Show filters" button at the top left-hand corner of the webpage.

!CellList.PNG|border=1!

# *Filters:* Show, hide or clear filters by clicking on these buttons
# *Current Filters:* Filters will show in the box once applied
# *Row Number:* The number of cells included in the filter criteria
# *Filter Criteria:* Filters are visual stimulus dependent (static grating, drifting grating, natural scene) and include: Orientation Selectivity (static or drifting gratings), Preferred Orientation (static or drifting gratings), Preferred direction (drifting grating), Preferred phase (static gratings), Preferred spatial frequency (static gratings), Preferred spatial frequency (drifting grating), Time to peak (static grating or natural scene), Preferred image (natural image)

More information can be found on these thumbnails and metrics from the [#Cell Detail Page]

h2. Cell Detail Page

Information at the level of the individual cell is available from the this page. Similar to the [#Experiment Detail Page] the top of the page provides metadata from the experiment from which this cell was imaged.


!CellMetadata.PNG!

For every {imagepopup:ImageName=StimulusDesign.png}*stimulus* {imagepopup}that the selected cell was responsive, a large thumbnail will be available to interact with. Hovering your mouse over the thumbnail will reveal the the selected visual stimulus. Each thumbnail also includes metrics calculated from the cell responses. Clicking on the "i" next to a visual stimulus will link to the webpage explaining both the stimulus as well as the thumbnail plot developed to describe the cellular response. Clicking on the stimulus in the table below will link to those same pages.

||*Visual Stimulus*|| *Thumbnail*|| *Metrics or Description*||
|*[Natural Scene|http://observatory.brain-map.org/visualcoding/stimulus/natural_scenes]*| Corona Plot| p-value, preferred image index, time to peak (s)|
|*[Drifting Grating|http://observatory.brain-map.org/visualcoding/stimulus/drifting_gratings]*| Star Plot| p-value, direction selectivity index, orientation selectivity index, preferred temporal frequency, preferred direction|
|*[Static Grating|http://observatory.brain-map.org/visualcoding/stimulus/static_gratings]*| Fan Plot| p-value, preferred phase, orientation selectivity index, preferred spatial frequency, preferred orientation (degrees), time to peak (s)|
|*[Natural Movies|http://observatory.brain-map.org/visualcoding/stimulus/natural_movies]*| Track Plots | five track plots demonstrate the cellular responses from the five movies shown to the mouse over the extent of the experiment|
|*[Locally Sparse Noise|http://observatory.brain-map.org/visualcoding/stimulus/locally_sparse_noise]*| Pincushion Plot| Plots indicating the receptive field for the On and Off subunits|
|*Speed Tuning*| | The mean change in response (% df/f) plotted against running speed (cm/s) during each session|

More information on the Visual Stimuli, Thumbnails and Metrics can be found in the Stimulus Set and Response Analysis whitepaper in [observatory:Documentation].