calciumImagingAnalysis (ciapkg) is a aoftware package for calcium imaging analysis of one- and two-photon imaging datasets.
See GitHub or https://git.io/ciapkg_docs for extensive README and details.
• Includes a GUI to allow users to do large-scale batch analysis, accessed via the repository's `calciumImagingAnalysis` class.
• The underlying functions can also be used to create GUI-less, command line-ready analysis pipelines.
• Includes major calcium imaging analysis steps: pre-processing (spatiotemporal downsampling, spatial filtering, relative fluorescence, etc.), multiple cell-extraction methods, cell classification (releasing soon!), cross-session cell alignment, and more.
• Includes code for determining animal position (e.g. in open-field assay).
• Supports Neurodata Without Borders (https://www.nwb.org/) data standard (see https://neurodatawithoutborders.github.io/matnwb/tutorials/html/ophys.html) for reading/writing cell-extraction (e.g. outputs of PCA-ICA, CELLMax, CNMF, CNMF-E, etc.). Supports reading NWB movie files (write support coming soon).
Note: not all File Exchange projects referenced in the "Acknowledgements" section are actively used in the repository, but many are used to perform specific functions. Either way, the code for each project is included within calciumImagingAnalysis for compatibility purposes and so users do not have to individually download them.
Biafra Ahanonu (2020). calciumImagingAnalysis (ciapkg) (https://github.com/bahanonu/calciumImagingAnalysis/releases/tag/v3.14.1), GitHub. Retrieved .
See release notes for this release on GitHub: https://github.com/bahanonu/calciumImagingAnalysis/releases/tag/v3.14.1