CaImAn an open source tool for scalable calcium imaging data analysis

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.…

• NS
  National Science Foundation

  Award: NeuroNex DBI-1707398
• PC
  Pew Charitable Trusts
• SF
  Simons Foundation
• GC
  Gatsby Charitable Foundation
• NI
  National Institutes of Health

  Awards: NIBIB R01EB022913, 1U19NS104648, R01-MH101198, 5U01NS090541, F32NS077840-01