CaImAn an open source tool for scalable calcium imaging data analysis.

TitleCaImAn an open source tool for scalable calcium imaging data analysis.
Publication TypeJournal Article
Year of Publication2019
AuthorsGiovannucci, A, Friedrich, J, Gunn, P, Kalfon, J, Brown, BL, Koay, SAnn, Taxidis, J, Najafi, F, Gauthier, JL, Zhou, P, Khakh, BS, Tank, DW, Chklovskii, DB, Pnevmatikakis, EA
Date Published2019 01 17
KeywordsAlgorithms, Animals, Artifacts, Brain, Calcium, Computational Biology, Data Analysis, Humans, Image Processing, Computer-Assisted, Mice, Microscopy, Fluorescence, Motion, Neurons, Observer Variation, Pattern Recognition, Automated, Photons, Reproducibility of Results, Software, Zebrafish

<p>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.</p>

Alternate JournalElife
PubMed ID30652683
PubMed Central IDPMC6342523
Grant ListF32 NS077840 / NS / NINDS NIH HHS / United States
NIBIB R01EB022913 / NH / NIH HHS / United States
R01 MH101198 / MH / NIMH NIH HHS / United States
R01 EB022913 / EB / NIBIB NIH HHS / United States
5U01NS090541 / NH / NIH HHS / United States
U19 NS104648 / NS / NINDS NIH HHS / United States
1U19NS104648 / NH / NIH HHS / United States
F32NS077840-01 / NH / NIH HHS / United States
R01-MH101198 / NH / NIH HHS / United States
U01 NS090541 / NS / NINDS NIH HHS / United States
FI-CCB / / Simons Foundation / International
SCGB / / Simons Foundation / International
NeuroNex DBI-1707398 / / National Science Foundation / International