# Ophys

This section contains information about the calcium imaging datasets. For these datasets,
neural activity was recorded using {term}`Two-photon calcium imaging`. Transgenic tools were
used to target the expression of a fluorescent calcium indicator, {term}`GCaMP`, to a
specific population of neurons. 

## Visual Coding

The [Visual Coding 2-photon](visual-coding/vc2p-background) dataset is a survey of in vivo physiological activity
in the awake mouse visual cortex. We collected data across six different visual cortical
areas, including {term}`V1` and five {term}`HVA`s, using 14 {term}`Transgenic line`s, and
across the cortical layers. During imaging, mice were awake, head-fixed under the microscope
and positioned on a running disk that enabled them to run at will (see [here](../../background/experimental-setup.md)). The mice passively viewed an assortment of [visual stimuli](visual-coding/vc2p-stimuli) presented on a monitor. 

## Visual Behavior

The [Visual Behavior Ophys](visual-behavior/VB-Ophys) dataset measured the activity of genetically identified neurons in the visual cortex of mice performing a go/no-go visual [Change Detection Task](change_detection_task). The same population of neurons was recorded over multiple days with varying sensory and behavioral contexts, including familiar and novel stimuli, and passive exposure sessions. This dataset can be used to evaluate the influence of experience, expectation, and task engagement on neural coding and dynamics in excitatory and inhibitory cell populations. 

## V1 Deep Dive

The [V1 Deep Dive](V1DD/V1DD-overview) dataset recorded data within a 800um X 800 um X 1mm volume within {term}`V1`. The experiment was similar to the Visual Coding dataset in that awake mice were imaged on a running disk, while viewing a set of passive [visual stimuli](V1DD/V1DD-stimuli) presented on a monitor. But we used a tiling method across many sessions to densely sample the entire volume. Calcium imaging data was collected from four mice, one of which was later imaged using Electron Microscopy for reconstruction.

## Brain Computer Interface