Work Description

Data for "Context flexibly modulates cue representations in visual cortex"

This repository contains data used in the paper "Context flexibly modulates cue representations in visual cortex" published in Nature Communications.

Abstract

Learning of cue-outcome associations and enacting appropriate behavioral responses is crucial for survival.
These learned, salient sensory cues ultimately result in enhanced responses in sensory cortices and, in turn, enhanced responses draw attention towards cues in our environment that guide future decision making.
To respond appropriately to these cues, one must recognize the cue but also the context.
How the identity of the sensory cue is encoded in cortex to facilitate detection in different contexts remains unclear.
Here we use chronic in vivo two-photon calcium imaging in visual cortex as mice learn a reward-based visual discrimination task and subsequently experience a change in external context through introduction of a threat stimulus.
We demonstrate that a visual stimulus associated with a reward elicits an enhanced response with learning, and that this enhanced response is due to newly recruited neurons responding preferentially to the rewarded cue in addition to neurons increasing the magnitude of their response.
Introduction of threat results in a largely separate set of neurons encoding the task cues, but the maintenance of the enhanced response to reward.
When the threat is relieved, the cue representations revert to the initial representations.
These data suggest that changes in an animal's external context can result in rapid but flexible shifts in the neural representation of learned cues.

Directory map


data/
├── raw/
│ ├── T07/
│ │ ├── T07_early_appetitive_001.sbx
│ │ ├── T07_early_appetitive_002.sbx
│ │ ├── T07_late_appetitive_001.sbx
│ │ └── ...
│ └── ...
└── processed/
├── sessions/
│ ├── T07/
│ │ ├── T07_early_appetitive.npz
│ │ ├── T07_late_appetitive.npz
│ │ └── ...
│ └── ...
│ └── crossday_neuron_indices.npz
├── heatmaps/
│ ├── single_day/
│ │ ├── heatmap_early_app_activated.mat
│ │ ├── heatmap_early_app_suppressed.mat
│ │ └── ...
│ └── crossday/
│ ├── heatmap_early_app_late_app_activated.mat
│ ├── heatmap_early_app_late_app_suppressed.mat
│ └── ...
└── pca/
├── trial_means.npz
└── trial_means_regressed_out.npz


Raw data (raw/)

File pattern: {mouse_id}/{mouse_id}_{condition}_{block}.sbx

Each file contains the raw recording for a particular mouse, condition, and block (either 001 or 002).
Each condition corresponds to a particular day, mainly consisting of two blocks (25k frames per block), with the exception of last_appetitive and threat_intro conditions which correspond to a single block.
These files have an .sbx extension, which is the native format for Scanbox, the MATLAB-based software we used for acquisistion of our calcium imaging.

Processed data (processed/)

Per-session data (processed/sessions/)

Individual sessions

File pattern: {mouse_id}/{mouse_id}_{condition}.npz

Cross-day matched neurons

File: crossday_neuron_indices.npz

Heatmaps (processed/heatmaps/)

Single-day heatmaps (processed/heatmaps/single_day/)

File pattern: heatmap_{condition}_{mode}.mat, where mode $\in$ {activated, suppressed}

Cross-day heatmaps (processed/heatmaps/crossday/)

File pattern: heatmap_{cond1}_{cond2}_{mode}.mat, where mode $\in$ {activated, suppressed}

PCA data (processed/pca/)

Files: trial_means.npz and trial_means_regressed_out.npz

Reference

• Alexa D. Faulkner and Alvin S. Chiu and Armin Sarabi and Swathi Karthik and Yaoxin S. Li and Christian R. Burgess. Context flexibly modulates cue representations in visual cortex. Nature Communications.
• Corresponding author: Christian R. Burgess.