Stimulus encoding by specific inactivation of cortical neurons

Neuronal ensembles are groups of neurons with correlated activity associated with sensory, motor, and behavioral functions. To explore how ensembles encode information, we investigated responses of visual cortical neurons in awake mice using volumetric two-photon calcium imaging during visual stimulation. We identified neuronal ensembles employing an unsupervised model-free algorithm and, besides neurons activated by the visual stimulus (termed “onsemble”), we also found neurons that are specifically inactivated (termed “offsemble”). Offsemble neurons showed faster calcium decay during stimuli, suggesting selective inhibition. In response to visual stimuli, each ensemble (onsemble+offsemble) exhibited small trial-to-trial variability, high orientation selectivity, and superior predictive accuracy for visual stimulus orientation, surpassing the sum of individual neuron activity. Thus, the combined selective activation and inactivation of cortical neurons enhance visual encoding as an eme..., Animals and surgery
All experimental procedures were conducted in accordance with the US National Institutes of Health and Columbia University Institutional Animal Care and Use Committee and were similar to our previous study14. Mice were housed in a controlled environment under a 12 h dark-light cycle at room temperature of ~23 °C and ~50% of humidity. Mice had ad libitum access to food and water. Experiments were performed in 12 adult transgenic mice (Slc17a7-IRES2-Cre, JAX stock # 023527) crossed with TIGRE2.0 Ai162 (TIT2L-GC6s-ICL-tTA2, JAX stock # 031562) maintained in C57BL/6 J congenic background. Mice were anesthetized with isoflurane (1.5–2%) while maintaining body temperature at 37 °C. Dexamethasone sodium phosphate (0.6 mg/kg) and Enrofloxacin (5 mg/kg) were administered subcutaneously and Carprofen (5 mg/kg) intraperitoneally. A titanium head-plate was attached to the skull, a 4 mm diameter craniotomy opened (center at 2.1 mm lateral and 3.4 mm posterior from bregma), and a ..., , # **Stimulus encoding by specific inactivation of cortical neurons**

## Description of the data and file structure

This dataset was generated by Jesús Pérez-Ortega, Alejandro Akrouh, and Rafael Yuste for the paper entitled \"**Stimulus encoding by specific inactivation of cortical neurons**\" published in Nature Communications [https://doi.org/10.1038/s41467-024-47515-x](https://doi.org/10.1038/s41467-024-47515-x). This folder has MATLAB data files of all mice, and each file contains the information of a single mouse session. The name of the file indicates the number of the mouse and the type of session. The letter \"S\" stands for spontaneous activity (blue screen), and the letter \"V\" stands for visual stimulation (8 directions of drifting gratings). For example, the file \"M3_V\" refers to the mouse number 3 during the visual stimulation session.
Every file is a MATLAB structure variable containing the information of the session (number of frames, sampling period, neuronal ROIs, raw signa...