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Behavioral Circuits and Sensory Processing3

Exploring the Brain in Action

Our brains are unfathomably complex. Yet, for most people, using them to walk down the street or recognize familiar objects requires little effort. In order to make sense of how neurons work together to produce these everyday actions, we need to record the activity from many neurons in different brain regions. As part of the Behavior Circuits and Sensory Processing project, we record neural activity in mice engaged in cycles of perception and action—and do it on a scale larger than any attempted previously. The Allen Brain Observatory presents the first standardized in vivo surveys of physiological activity in the mouse visual cortex. Dedicated teams carry out each step of the protocol as mice are prepared for experiments, cortical areas are mapped, and neural activity is recorded in response to a wide set of visual stimuli (schematized below). The collected data is processed and stored systematically, and finally packaged using a standard data format, Neurodata Without Borders (NWB). We make all of the data from our systematic surveys of the mouse visual system available to the community for further analysis and exploration. These data provide a rich testbed for theories and models of cortical computation.

Visual Coding

Using a broad range of visual stimuli, ranging from gratings and noise stimuli to natural images and movies, we have surveyed the spatial and temporal dynamics of visual representation in the mouse corticothalamic visual pathways. Some of the questions these data can be used to address include: How are signals from the outside world represented in the brain, and how are signals relayed between brain regions? Why is it important for mice (and humans) to have many visual areas? What role do different cell types play in processing visual information? 

2-Photon Imaging

Using transgenically expressed GCaMP6 restricted to specific populations of neurons, we have recorded the visual responses from over 63,000 neurons from 14 transgenic lines, across 6 cortical areas and 4 cortical layers. The spatial and temporal dynamics of the visual responses are measured using a diverse set of visual stimuli. Calcium imaging enables large populations of hundreds of neurons to be imaged simultaneously, allowing the interactions of neurons to be explored.


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Using state-of-the-art implantable probes, called Neuropixels, we have recorded the spiking activity of nearly 100,000 neurons from wild-type mice and 3 transgenic lines, across a variety of regions in the cortex, hippocampus, and thalamus. We use a similar set of stimuli to the 2P Imaging Observatory to facilitate a direct comparison between these two datasets. A key feature of these experiments is our ability to record simultaneously across as many as 8 visual regions, which will enable scientists to study inter-areal neural communication patterns in greater detail than ever before.

Learn more about our Neuropixels experiments

Visual Behavior

We have used large-scale physiological recordings in behaving animals to characterize how sensation and behavior are encoded in activity across the visual cortex and how these representations are influenced by behavior state, expectation, and experience during an image change detection task. Just like the Visual Coding project, the Visual Behavior project leverages the Allen Brain Observatories to collect highly standardized datasets. 

This dataset can be used to address questions such as: How do different types of neurons in the brain encode sensory and behavioral information? Are these representations flexible depending on motivation or expectation? How are interactions across cortical areas and depths modified by experience? 

2-Photon Imaging

Using single- and multi-plane 2-photon calcium imaging in the visual cortex of transgenic mice expressing the calcium indicator GCaMP6f in populations of excitatory and inhibitory neurons, we have recorded neural activity during performance of a visual change detection task from 34,619 neurons in 551 in vivo imaging sessions. A key aspect of the experimental design is the repeated imaging of the same populations of neurons across multiple days, allowing analysis of single cell changes across behavioral and sensory conditions, including task engagement and stimulus novelty.

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Additional Datasets

Ophys/Ephys Calibration Data

This dataset consists of simultaneously measured fluorescence and spiking activity of pyramidal neurons in layer 2/3 of primary visual cortex in transgenic mouse lines expressing genetically-encoded calcium indicators (GECIs) GCaMP6s or GCaMP6f.

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Additional Resources

  • Neurodata Without Borders - Learn more about the format we use to store our publicly available neurophysiology data.

  • Neuropixels - Purchase the probes we use to record action potentials throughout the mouse brain.

  • Open Ephys GUI - Download the open-source software we use to collect Neuropixels data.