Skip to end of metadata
Go to start of metadata

Neuronal Response: Two-Photon Calcium Imaging

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.

Searching the Data

The data can be searched either by experiment or by cellular response. To search for a specific experiment or to search for cells that respond to a specific visual stimulus, click on the respective Experiments tab or Cells tab from the menu banner. Characterization of the transgenic mouse lines used in this study is available from the Transgenic Characterization tab.

Exploring the Data from the Interactive Landing Page

The Allen Brain Observatory 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.

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

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.

From the landing page, you can explore the transgenic mouse line, cortical area and cortical depth of the experiments conducted in this study. Hovering your mouse over the transgenic lines, cortical area or cortical depth will highlight the parameters captured in the experiments of this study. Clicking on one of these interactive links will return a Cell Search with those specific criteria.

Experiment Design

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”). Each experiment includes three imaging sessions as illustrated below. Data released in the June 2016 and October 2016 releases were collected using sessions A, B and C.  Data released in the June 2017 release were collected using sessions A, B and C2.

For more information on the experimental design and the visual stimulus set, see the Stimulus Set and Response Analysis whitepaper in Documentation.

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

RLVISrlRostrolateral visual area
AMVISamAnteromedial visual area

*Wang and Burkhalter (J.Comp.Neurol., 502: 339-357. doi: 10.1002/cne.21286)

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

Fluorescent 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 Documentation.

New info on transgenic lines? Link to paper?

Experiment Search

Clicking "Experiments" in the menu banner will take you to a Experiment Search page. By default, all experiments conducted in this study are listed on this page. The list of experiments can be sorted/filtered by clicking the "Show Filters" button which opens options for selecting experiments by Brain Area (VISal, VISp, VISl, VISpm, VISam, VISrl), Imaging Depth in microns (175, 265, 275, 300, 320, 335, 350, 365, 375, 435) or by Cre Driver (Rbp4-Cre_KL100, Cux2-CreERT2, Emx1-IRES-Cre, Scnn1a-Tg3-Cre, Rorb-IRES2-Cre, Nr5a1-Cre).

Each experiment is displayed by a row in the results list below the Filters menu. All of the columns (minus the two common mouse lines) are displayed by default. Columns can be hidden by deselecting them from the drop-down menu. The population thumbnails are segregated by visual stimulus as indicated by the stimulus color key. Overall cell population responses of the neurons in the imaging field of view to a specific visual stimuli are displayed as population thumbnails and can be explored in more detail from the Experiment Detail Page. More information on how these features were computed can be found in the Stimulus Set and Response Analysis whitepaper located in Documentation.

 

 

Name

Description

 

Experiment ID

Clicking this link will open the Experiment Detail Page

 

Brain Area

Brain Area imaged (VISal, VISp, VISl, VISpm, VISam, VISrl)

 

Cre Driver 1

Cre Driver line used (Rbp4-Cre_KL100, Cux2-CreERT2, Emx1-IRES-Cre, Scnn1a-Tg3-Cre, Rorb-IRES2-Cre, Nr5a1-Cre)

 Cre Driver 2Currently all experiments are conducted with Camk2a as Cre Driver 2
 ReporterCurrently all experiments are conducted with Ai93(TITL-GCaMP6f) as the Reporter line

 

Imaging Depth

Imaging depth in microns (175, 265, 275, 300, 320, 335, 350, 365, 375, 435)

 

Cells

clicking this link will open a Cell Search page with cell responses from this experiment

 

Experiment

Shows an image of cells captured in this field of view in this experiment - clicking will open the Experiment Detail Page

a & g

Orientation Selectivity

Cumulative histogram plot of orientation selectivity of responsive cells during the static and drifting gratings stimuli

b

Preferred Spatial Frequency

Histogram plotting the preferred spatial frequency of responsive cells during the static gratings stimulus

c

Preferred Orientation

Semi-pie chart showing the preferred orientation of responsive cells during the static gratings stimulus

d & k

Time to Peak

Temporal dynamics of the mean response of responsive cells to the static grating and natural scenes stimuli

e, j & lRepresentational SimilarityA heat map showing the response similarity in evoked responses from the static gratings, drifting gratings and natural scenes

f

Direction Selectivity

Cumulative histogram plot of direction selectivity of responsive cells during the drifting gratings stimulus

h

Preferred Direction

Pie chart showing the preferred direction of responsive cells during the drifting gratings stimulus

i

Preferred Temporal Frequency

Histogram plotting the preferred temporal frequency of responsive cells during the drifting gratings stimulus

mPopulation Receptive FieldComputed heat map of all the On and Off subunits mapped in this experiment
n & oSignal/Noise CorrelationScatter plots comparing the signal and noise correlations in response to drifting gratings or static gratings and natural scenes
p, q & rEye Positions (A, B, C)Density plot of eye positions during sessions A, B & C
s, t & uRunning Speed (A, B, C)Histogram plotting the running speed (cm/s) over time during sessions A, B & C

Experiment Detail Page

Each experiment is composed of three approximately one-hour two-photon calcium imaging sessions.The experiment detail page presents a more detailed view of each experiment including experiment meta-data, summary images of the cortical field of view in each experiment and the calculated cell population features and metrics as represented by the population thumbnails.

Experimental Metadata and Summary Images

Metadata for the experiment is listed at the top of the page including the driver and reporter lines for each transgenic line, targeted functional visual area, imaging depth, a link to the Cell List - which summarizes the cell responses for each of the two-photon calcium imaging sessions, the Experiment ID, the mouse genotype and any notes important for the user to know about this transgenic line. Summary images of the cortical field of view from each of the imaging sessions are included under the metadata.


Population Thumbnails

Below the summary images and metadata are large versions of each of the population thumbnails shown on the Experiment Search 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)

 Representational SimilarityHeat map of response similarity to drifting gratings

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

 Representational SimilarityHeat map of response similarity to static gratings

Natural Scene

Time to Peak

Temporal dynamics of the mean response time of the responsive cells

 Population Receptive FieldHeat map of the sum of all On and Off subunits
 Representational SimilarityHeat map of response similarity to natural scenes
Experiment SummariesSignal and Noise Correlations - Session AScatter-plot showing comparisons of signal and noise correlations in response to drifting gratings
 Signal and Noise Correlations - Session BScatter-plot showing comparisons of signal and noise correlations in response to stating gratings  and natural scenes
 Eye Position - Sessions A, B, CDensity plot of eye positions during each recording session
 Running Speed - Sessions A, B, CHistogram summarizing the running spead (cm/s) over time for each recording session

Cell Search

Clicking the "Cells" tab from the menu banner will open a search page from which all the cells from every experiment can be filtered and sorted. Clicking the interactive panels from the Allen Brain Observatory landing page or the "View Cells" link from an Experiment Detail Page will open the Cell Search page with filtering already pre-set.

Cell List

This page displays the cellular response summaries of a cell search with one cell per row. Clicking anywhere on a row will take you to the Cell Detail Page. 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 page.

Sorting Cells

By default the cells are sorted based on the significance of their measured responses to presentation of the static grating, listed here as their p-value, but can also be sorted by several other parameters from the "Sort" drop-down menu. The list of cells includes metadata on the experiment (Brain area, Cre driver, Imaging depth) and 23 response summaries (including visualizations and computed metrics) to the various visual stimuli. Of the 23 columns available, only 18 are displayed by default, but can be displayed from the "Add/Remove Columns" drop down menu in the filters box. Sorting is based on the calculated features derived from the cellular responses to the visual stimuli.

 Column HeaderDescription
 Experiment IDClicking this link opens the Experiment Detail Page for the specific experiment (not shown by default)
 Brain AreaBrain Area imaged (VISal, VISp, VISl, VISpm, VISam, VISrl)
 Cre Driver 1Cre Driver line used (Rbp4-Cre_KL100, Cux2-CreERT2, Emx1-IRES-Cre, Scnn1a-Tg3-Cre, Rorb-IRES2-Cre, Nr5a1-Cre)
 Cre Driver 2Currently all experiments are conducted with Camk2a as Cre Driver 2 (not shown by default)
 ReporterCurrently all experiments are conducted with Ai93(TITL-GCaMP6f) as the Reporter line (not shown by default)
 Imaging DepthImaging depth in microns (175, 265, 275, 300, 320, 335, 350, 365, 375, 435)
aStatic GratingsFan plot summarizing the cell responses to the static grating stimulus and the calculated features: p-value (p), orientations selectivity index (osi), global orientation selectivity (g-osi), preferred orientation (po), preferred phase (pp), preferred spatial frequency (psf), time to peak (ttp), peak DF/F (df/f)
bDrifting GratingsStar plot summarizing the cell responses to the drifting grating stimulus and the calculated features: p-value (p), orientations selectivity index (osi), global orientation selectivity (g-osi), preferred direction (pd), direction selectivity index (dsi), global direction selectivity index (g-dsi), preferred temporal frequency (ptf), peak DF/F (df/f)
cCell Receptive Field - Off/OnReceptive field plot showing the pixels that elicit a significant response to off stimuli (black spot on mean luminance grey background) or on stimuli (white spot on mean luminance grey background) and the calculated features: receptive field chi2 (chi2), receptive field off (off), receptive field on (on), receptive field overlap index (ov)
dLocally Sparse Noise - offThe "Pincushion" plot is a representation of cell responsiveness to the visual receptive field for Off stimuli (a black spot on a mean luminance grey background). For each location in visual space, all of the trials (~115) for an Off stimulus are ranked and represented as dots, where the relative intensity of blue hue corresponds to the strength of the cell response during that trial. (not shown by default)
eLocally Sparse Noise - onThe "Pincushion" plot is a representation of cell responsiveness to the visual receptive field for On stimuli (a white spot on a mean luminance grey background). For each location in visual space, all of the trials (~115) for an On stimulus are ranked and represented as dots, where the relative intensity of red hue corresponds to the strength of the cell response during that trial. (not shown by default)
fNatural ScenesCorona plot summarizing the cell responses to stimuli by 118 natural images over 50 trials and the calculated features: p-value (p), preferred scene (pii), time to peak (ttp), peak DF/F (df/f), image selectivity (is)
gNatural movie 1A, 1B, 1C, 2, 3Track plot summarizing cell responses to either a 30 sec movie (1A, 1B, 1C, 2) or a 120 sec movie (3) and the calculated response reliability (rel)
hSpeed Tuning A, B, CThis graph plots the mean df/f of a cell as a function of it's running speed (cm/s) when visual stimuli are being presented (red trace) or during spontaneous activity (blue trace) from all 3 imaging sessions
i & jSignal Correlation A, BThis plot shows the distribution of signal correlations between this cell's responses to drifting gratings (from Session A) or static gratings and natural scenes (from Session B) and the responses of other cells in the same experiment.

 

 

Filtering Cells

To filter the cells based on cellular responses across all the experiments, first click on the "Show filters" button at the top left-hand corner of the webpage.

  1. Filters: Show, hide or clear filters by clicking these buttons
  2. Sort: Sort by parameter and choose either ascending or descending sort
  3. Add/Remove Columns: Increase or decrease the number of columns shown in your cell search results
  4. Current Filters: Filters will show in the box once applied
  5. Filter Parameters: Clicking a radio box will determine which visual stimulus or metadata parameters you can filter on
  6. Filter Criteria: Parameters are visual stimulus and metadata dependent. Cell metadata parameters are Brain area, Imaging depth and Cre-driver. You can also limit the data results to cells with data in all columns from this search. Visual stimulus parameters are as follows: p-value (all visual stimuli), 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 temporal frequency (drifting grating), Time to peak (static grating or natural scene), Preferred image (natural image),
  7. Row Number: The number of cells included in the filter criteria
    More information can be found on these thumbnails and metrics from the Cell Detail Page

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.

For every stimulus that the selected cell was responsive to, 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 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

Corona Plot

p-value, preferred image index, time to peak (s)

Drifting Grating

Star Plot

p-value, direction selectivity index, orientation selectivity index, preferred temporal frequency, preferred direction

Static Grating

Fan Plot

p-value, preferred phase, orientation selectivity index, preferred spatial frequency, preferred orientation (degrees), time to peak (s)

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

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 Documentation.

 

  • No labels