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OnACID: Online Analysis of Calcium Imaging Data in Real Time
Andrea Giovannucci · Johannes Friedrich · Matt Kaufman · Anne Churchland · Dmitri Chklovskii · Liam Paninski · Eftychios Pnevmatikakis

Tue Dec 05 06:30 PM -- 10:30 PM (PST) @ Pacific Ballroom #146

Optical imaging methods using calcium indicators are critical for monitoring the activity of large neuronal populations in vivo. Imaging experiments typically generate a large amount of data that needs to be processed to extract the activity of the imaged neuronal sources. While deriving such processing algorithms is an active area of research, most existing methods require the processing of large amounts of data at a time, rendering them vulnerable to the volume of the recorded data, and preventing real-time experimental interrogation. Here we introduce OnACID, an Online framework for the Analysis of streaming Calcium Imaging Data, including i) motion artifact correction, ii) neuronal source extraction, and iii) activity denoising and deconvolution. Our approach combines and extends previous work on online dictionary learning and calcium imaging data analysis, to deliver an automated pipeline that can discover and track the activity of hundreds of cells in real time, thereby enabling new types of closed-loop experiments. We apply our algorithm on two large scale experimental datasets, benchmark its performance on manually annotated data, and show that it outperforms a popular offline approach.

Author Information

Andrea Giovannucci (Flatiron Institute, Simons Foundation)

Andrea Giovannucci joined the Center for Computational Biology as a data scientist in the neuroscience group in 2015. He is responsible for the development of calcium imaging software, general-purpose neural networks and other potential data-intensive computing projects. Prior to joining the foundation, Giovannucci was a post-doctoral fellow at the Neuroscience Institute at Princeton University. He has a Ph.D. in computer science from Universitat Autònoma de Barcelona in Spain and a B.S. in electronic engineering from Politecnico di Milano in Italy.

Johannes Friedrich (Columbia University)
Matt Kaufman (Cold Spring Harbor Laboratory)
Anne Churchland (Cold Spring Harbor Laboratory)
Dmitri Chklovskii (Simons Foundation)
Liam Paninski (Columbia University)
Eftychios Pnevmatikakis (Flatiron Institute)

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