title: Fast online deconvolution of calcium imaging data.
abstract: Fluorescent calcium indicators are a popular means for observing the spiking activity of large neuronal populations, but extracting the activity of each neuron from raw fluorescence calcium imaging data is a nontrivial problem. We present a fast online active set method to solve this sparse non-negative deconvolution problem. Importantly, the algorithm 3progresses through each time series sequentially from beginning to end, thus enabling real-time online estimation of neural activity during the imaging session. Our algorithm is a generalization of the pool adjacent violators algorithm (PAVA) for isotonic regression and inherits its linear-time computational complexity. We gain remarkable increases in processing speed: more than one order of magnitude compared to currently employed state of the art convex solvers relying on interior point methods. Unlike these approaches, our method can exploit warm starts; therefore optimizing model hyperparameters only requires a handful of passes through the data. A minor modification can further improve the quality of activity inference by imposing a constraint on the minimum spike size. The algorithm enables real-time simultaneous deconvolution of O(105) traces of whole-brain larval zebrafish imaging data on a laptop.
authors.affiliation: Department of Statistics, Grossman Center for the Statistics of Mind, and Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America.|Janelia Research Campus, Ashburn, Virginia, United States of America.
authors.forename: Johannes
authors.identifier: 0000-0002-1321-5866
authors.initials: J
authors.lastname: Friedrich
authors.affiliation: Department of Statistics, Grossman Center for the Statistics of Mind, and Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America.|Center for the Neural Basis of Cognition and Machine Learning Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.
authors.forename: Pengcheng
authors.initials: P
authors.lastname: Zhou
authors.affiliation: Department of Statistics, Grossman Center for the Statistics of Mind, and Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America.|Kavli Institute for Brain Science, and NeuroTechnology Center, Columbia University, New York, New York, United States of America.
authors.forename: Liam
authors.initials: L
authors.lastname: Paninski
mesh_terms: D000818:Animals; D002118:Calcium / Q000378:metabolism*; D020013:Calcium Signaling / Q000502:physiology*; D003627:Data Interpretation, Statistical; D006801:Humans; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D008856:Microscopy, Fluorescence / Q000379:methods; D057054:Molecular Imaging / Q000379:methods*; D009474:Neurons / Q000166:cytology / Q000502:physiology*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D056969:Voltage-Sensitive Dye Imaging / Q000379:methods*
chemical_list: D002118:Calcium