CaImAn an open source tool for scalable calcium imaging data analysis

Andrea Giovannucci, Johannes Friedrich, Pat Gunn, Jérémie Kalfon, Brandon L. Brown, Sue Ann Koay, Jiannis Taxidis, Farzaneh Najafi, Jeffrey L. Gauthier, Pengcheng Zhou, Baljit S. Khakh, David W. Tank, Dmitri B. Chklovskii, Eftychios A. Pnevmatikakis

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. We present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good scalability on computers ranging from laptops to high-performance computing clusters. CaImAn is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data. To benchmark the performance of CaImAn we collected and combined a corpus of manual annotations from multiple labelers on nine mouse two-photon datasets. We demonstrate that CaImAn achieves near-human performance in detecting locations of active neurons.

Original languageEnglish (US)
JournaleLife
Volume8
DOIs
StatePublished - Jan 17 2019

Fingerprint

Alligators and Crocodiles
Photons
Calcium
Imaging techniques
Cluster computing
Fluorescence microscopy
Computing Methodologies
Neurons
Scalability
Brain
Benchmarking
Pipelines
Fluorescence Microscopy
Monitoring
Libraries
Processing

All Science Journal Classification (ASJC) codes

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Keywords

  • calcium imaging
  • data analysis
  • mouse
  • neuroscience
  • one-photon
  • open source
  • software
  • two-photon
  • zebrafish

Cite this

Giovannucci, A., Friedrich, J., Gunn, P., Kalfon, J., Brown, B. L., Koay, S. A., ... Pnevmatikakis, E. A. (2019). CaImAn an open source tool for scalable calcium imaging data analysis. eLife, 8. https://doi.org/10.7554/eLife.38173
Giovannucci, Andrea ; Friedrich, Johannes ; Gunn, Pat ; Kalfon, Jérémie ; Brown, Brandon L. ; Koay, Sue Ann ; Taxidis, Jiannis ; Najafi, Farzaneh ; Gauthier, Jeffrey L. ; Zhou, Pengcheng ; Khakh, Baljit S. ; Tank, David W. ; Chklovskii, Dmitri B. ; Pnevmatikakis, Eftychios A. / CaImAn an open source tool for scalable calcium imaging data analysis. In: eLife. 2019 ; Vol. 8.
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Giovannucci, A, Friedrich, J, Gunn, P, Kalfon, J, Brown, BL, Koay, SA, Taxidis, J, Najafi, F, Gauthier, JL, Zhou, P, Khakh, BS, Tank, DW, Chklovskii, DB & Pnevmatikakis, EA 2019, 'CaImAn an open source tool for scalable calcium imaging data analysis', eLife, vol. 8. https://doi.org/10.7554/eLife.38173

CaImAn an open source tool for scalable calcium imaging data analysis. / Giovannucci, Andrea; Friedrich, Johannes; Gunn, Pat; Kalfon, Jérémie; Brown, Brandon L.; Koay, Sue Ann; Taxidis, Jiannis; Najafi, Farzaneh; Gauthier, Jeffrey L.; Zhou, Pengcheng; Khakh, Baljit S.; Tank, David W.; Chklovskii, Dmitri B.; Pnevmatikakis, Eftychios A.

In: eLife, Vol. 8, 17.01.2019.

Research output: Contribution to journalArticle

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AU - Friedrich, Johannes

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AU - Kalfon, Jérémie

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AU - Taxidis, Jiannis

AU - Najafi, Farzaneh

AU - Gauthier, Jeffrey L.

AU - Zhou, Pengcheng

AU - Khakh, Baljit S.

AU - Tank, David W.

AU - Chklovskii, Dmitri B.

AU - Pnevmatikakis, Eftychios A.

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Giovannucci A, Friedrich J, Gunn P, Kalfon J, Brown BL, Koay SA et al. CaImAn an open source tool for scalable calcium imaging data analysis. eLife. 2019 Jan 17;8. https://doi.org/10.7554/eLife.38173