Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 73,219 bioRxiv papers from 318,728 authors.

OnACID: Online Analysis of Calcium Imaging Data in Real Time

By Andrea Giovannucci, Johannes Friedrich, Matthew T. Kaufman, Anne Churchland, Dmitri Chklovskii, Liam Paninski, Eftychios A. Pnevmatikakis

Posted 02 Oct 2017
bioRxiv DOI: 10.1101/193383

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.

Download data

  • Downloaded 2,206 times
  • Download rankings, all-time:
    • Site-wide: 2,283 out of 73,229
    • In neuroscience: 345 out of 13,158
  • Year to date:
    • Site-wide: 17,626 out of 73,229
  • Since beginning of last month:
    • Site-wide: 17,626 out of 73,229

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)