Calcium Imaging Data Analysis
End-to-end analysis pipeline for longitudinal in vivo calcium imaging.
Overview
Raw recordings from mouse motor cortex are motion-corrected and run through CNMF-E (via Mesmerize/CaImAn) to extract and denoise each neuron’s activity. The pipeline then normalizes the traces, runs peak detection to find calcium transients, builds pairwise correlation matrices, and clusters neurons by activity features. It batch-processes large longitudinal datasets across animals and imaging days, comparing sham vs. stroke and stim vs. no-stim groups.
Used in Kopchock III et al. 2026.