OnACID: Online analysis of calcium imaging data in real time

Giovannucci, A., Friedrich, J., Kaufman, M., Churchland, A. K., Chklovskii, D., Paninski, L., Pnevmatikakis, E. A. (December 2017) OnACID: Online analysis of calcium imaging data in real time. 31st Annual Conference on Neural Information Processing Systems, NIPS 2017;, 2017-D. pp. 2382-2392. ISSN 10495258

URL: http://papers.nips.cc/paper/6832-onacid-online-ana...

Abstract

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. © 2017 Neural information processing systems foundation. All rights reserved.

Item Type: Paper
Uncontrolled Keywords: Benchmarking Calcium Neurons Closed-loop experiments Imaging experiments Large amounts of data Motion artifact corrections Neuronal populations Online dictionary learning Optical imaging method Processing algorithms Image processing
Subjects: organs, tissues, organelles, cell types and functions > sub-cellular tissues: types and functions > calcium channel
Investigative techniques and equipment > imaging
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons > neuronal circuits
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons > neuronal circuits
organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons > neuronal circuits
CSHL Authors:
Communities: CSHL labs > Churchland lab
Depositing User: Matt Covey
Date: December 2017
Date Deposited: 01 Jun 2018 20:31
Last Modified: 01 Jun 2018 20:31
URI: http://repository.cshl.edu/id/eprint/36701

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