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Name

Description

 

Experiment ID

clicking 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

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

Experimental Metadata and Summary Images

Metadata for the experiment is listed at the top of the page including the driver and reporter 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.

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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

Cell List

This page displays the cellular response summaries 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. Clicking the "Cells" 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.

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Sorting Cells

 

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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.

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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.

 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)
 Static 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)
 Drifting 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)
 Cell Receptive Field - OffReceptive field plot showing the pixels that elicit a significant response to off stimuli (black spot on mean luminance grey background)
 Cell Receptive Field - OnReceptive field plot showing the pixels that elicit a significant response to on stimuli (white spot on mean luminance grey background)
 Locally 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)
 Locally 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)
 Natural ScenesCorona plot summarizing the cell responses to stimuli by 118 natural images over 50 trials
 Natural 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)
 Speed 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
 Signal 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.

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