PHYSION: AN INTEGRATED SOFTWARE FOR THE ACQUISITION, ANALYSIS AND SHARING OF NEUROPHYSIOLOGICAL RECORDINGS DURING VISUAL PROCESSING IN AWAKE MICE

Studies combining neurophysiological and behavioral measurements often generate heterogeneous data formats by design. Although this heterogeneity impedes large-scale analysis and cross-experiment comparisons, and substantially limits data reuse, data standardization offers a clear remedy: it promotes reusability and enables analysis tools built on standardized data to be readily adopted across the scientific community. Here, we introduce Physion, an integrated, modular software for data acquisition, analysis, and sharing of cellular and circuit physiology data for visual processing in behaving mice. The software assembles all pre-processed signals, stimulus information, timestamps, and metadata into the Neurodata Without Borders (NWB) format, ensuring compatibility with existing tools in the NWB ecosystem. Using Physion, we acquired two-photon calcium imaging recordings from excitatory and inhibitory neurons in mouse V1 during repeated presentations of a battery of visual stimulations and pre-processed them with the suite2p pipeline. Here we show, through Physion, how to i) align fluorescence and behavioral signals to stimulus onsets and store them in NWB files; ii) obtain ΔF/F traces by using computational methods that are specific for distinct neuron types; and iii) quantify neuronal responses to behavioral states on a trial-by-trial basis. Physion, designed for integration with the scientific computing toolkit in python (numpy, scipy, scikit-learn...), provides a user-friendly API for flexible visualization and analysis and generates summary metrics including response amplitude and reliability, stimulus selectivity and behavioral state modulation. Together, this workflow facilitates the sharing and reuse of complex visual cortex datasets and offers a template for integrating neurophysiology data into FAIR-compliant, large-scale neuroscience resources.