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Visual Coding - 2p

2-Photon Calcium Imaging

2-photon calcium imaging enables the activity of hundreds of neurons to be recorded simultaneously. A calcium indicator (GCaMP6) fluoresces whenever neurons are fire spikes. Here, we use transgenic tools to drive the expression of this fluorescent calcium indicator in specific populations of Cre-defined neurons. Post-hoc image processing identifies somatic ROIs and extracts the fluorescence of these neurons for further analysis.


The Visual Coding - 2P dataset has recorded the activity of populations of neurons throughout the mouse visual cortex, sampling from distinct cell populations, using a standardized set of visual stimuli. Data for each experiment is conveniently packaged in NWB files that can be downloaded via the AllenSDK and is also available as an AWS Public Dataset. In addition, the raw movies are available on AWS. 

Visual Coding - 2P dataset

Using transgenically expressed GCaMP6 restricted to specific populations of neurons, we have sampled responses from 14 transgenic lines, across 6 cortical areas and 4 cortical layers. In total 63,251 neurons have been imaged. 

Cre lines include:

  • Pan-excitatory:

Emx1-IRES-Cre, Slc17a7-IRES2-Cre

  • Specific excitatory populations:

Cux2-CreERT2 ; Rorb-IRES2-Cre; Scnn1a-Tg3-Cre; Nr5a1-Cre; Rbp4-Cre; Tlx3-Cre; Fezf-CreER; Ntsr1-Cre

  • Inhibitory interneurons:

Vip-IRES-Cre; Sst-IRES-Cre; Pvalb-IRES-Cre

More information on Cre lines used in this dataset is available here

Data was collected from primary visual cortex (VISp) and five higher visual areas (VISl, VISal, VISpm, VISam, VISrl).


Visual stimuli

Diverse but well-studied visual stimuli were presented to awake mice in a passive viewing condition. Stimuli included many traditional stimuli such as gratings and locally sparse noise to characterize traditional tuning curves and receptive field properties, as well at natural scenes and movies that have more diverse features and natural statistics. The stimuli were presented in three one-hour imaging sessions per population of neurons.