Extracting large-scale neural activity with Suite2p

Abstract Neural recordings using optical methods have improved dramatically. For example, we demonstrate here recordings of over 100,000 neurons from the mouse cortex obtained with a standard commercial microscope. To process such large datasets, we developed Suite2p, a collection of efficient algorithms for motion correction, cell detection, activity extraction and quality control. We also developed new approaches to benchmark performance on these tasks. Our GPU-accelerated non-rigid motion correction substantially outperforms alternative methods, while running over five times faster. For cell detection, Suite2p outperforms the CNMF algorithm in Caiman and Fiola, finding more cells and producing fewer false positives, while running in a fraction of the time. We also introduce quality control steps for users to evaluate performance on their own data, while offering alternative algorithms for specialized types of recordings such as those from one-photon and voltage imaging. Competing Interest Statement The authors have declared no competing interest.