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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 , and 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
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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.
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:
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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.clicking on the individual "Visual Stimuli" thumbnails below the cortical imaging locations.
The landing page shows a visual summary of the dataset contents. Transgenic mouse lines (left panel) were selected based on the subpopulation of neurons expressing GCamp6. 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 one of these interactive links will return a Cell Search with those specific criteria.
Targeted Functional Visual Areas
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- Cux2-CreERT2
- Rorb-IRES2-Cre
- Rbp4-Cre_KL100
- Nr5a1-Cre
- Scnn1a-Tg3-Cre
- Emx1-IRES-Cre
Fluorescent Histological characterization of for 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.
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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 detailed experiment meta-datainformation, 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 Detailed information about each 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, including mouse genotype information, cortical area imaging depth that the data was acquired from, 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 lineand experimental series identifier. Some experiments will have notes with information about special considerations, such as animal physiology. Summary images of the cortical field of view from each of the imaging sessions are included under the metadataalso shown.
Population Thumbnails
Below the summary images and metadata are large versions of each of the population thumbnails The cortical field of view that is captured in a single imaging session is referred to as the “population” of cells that are recorded simultaneously. Population image thumbnails are shown on the Experiment Search page, with a description of what the thumbnail representsthe data that may be available from each of these sessions.
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Visual Stimulus | Thumbnail | Description |
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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 Similarity | Heat 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 Similarity | Heat 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 Field | Heat map of the sum of all On and Off subunits | |
| Representational Similarity | Heat map of response similarity to natural scenes | |
| Experiment Summaries | Signal and Noise Correlations - Session A | Scatter-plot showing comparisons of signal and noise correlations in response to drifting gratings |
| Signal and Noise Correlations - Session B | Scatter-plot showing comparisons of signal and noise correlations in response to stating gratings and natural scenes | |
| Eye Position - Sessions A, B, C | Density plot of eye positions during each recording session | |
| Running Speed - Sessions A, B, C | Histogram summarizing the running spead (cm/s) over time for each recording session |
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