Realtime analysis of fluorescence imaging data

Optical imaging methods using fluorescence 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. In this talk I will describe CaImAn Online, a 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.

Dr. Andrea Giovannucci is an Assistant Professor in Neural Engineering at the UNC/NCSU department of Bioengineering. Prior to this appointment, Dr. Giovannucci was a machine learning data scientist at the Flatiron Institute (Simons Foundation) and a postdoctoral fellow (experimental neuroscience) at the Princeton Neuroscience Institute. Dr. Giovannucci obtained his PhD in artificial intelligence from the Autonoma University of Barcelona and the Artificial Intelligence Research Institute of Bellaterra (IIIA-CSIC), Spain. Dr. Giovannucci is affiliated with the UNC/NCSU joint Bioengineering department, the Closed-loop Engineering for Advanced Rehabilitation (CLEAR) and the UNC Neuroscience Center.