CaImAn documentation

Contents:

• Overview
  • Companion paper
  • Developers/Contributors
  • Questions, comments, issues
  • License
• Installation and Updating
  • Installing CaImAn
  • Package-based Process
    • Known issues
  • Development mode Installation Process
    • Installation on Windows
    • Installation on MacOS and Linux
    • Setting up environment variables
  • Setting up caimanmanager
  • Upgrading
    • Upgrading the conda-forge package
    • Upgrading and source-based installations
    • Upgrading and caiman_data
  • Installing additional packages
• What’s new?
  • Online analysis for microendoscopic 1p data (January 2020)
  • Analysis pipeline for Voltage Imaging data (December 2019)
  • Installation through conda-forge (August 2019)
  • Exporting results, GUI and NWB support (July 2019)
• Getting Started with CaImAn
  • Demos
  • Basic Structure
  • Parameters
  • Component evaluation
  • Result Interpretation
  • Result variables for 2p batch analysis
  • Variables for component evaluation
  • Variables for 1p processing (CNMF-E)
  • Variables for online processing
• Handling movies
  • Loading movies
  • Saving movies
  • Visualizing movies
  • Manipulating movies
    • concatenation
    • movie resizing
• CaImAn Tips
  • Motion Correction tips
  • CaImAn Online Processing tips
  • CaImAn Batch processing tips
  • 1p processing tips
  • Deconvolution tips
• On file types and sizes
• Graphical interfaces
  • The CaImAn GUI
  • External interfaces
• Features
  • References
    • Software package detailed description and benchmarking
    • Deconvolution and demixing of calcium imaging data
    • Online Analysis
    • Motion Correction
    • Behavioral Analysis
    • Variance Stabilization
    • Voltage imaging
• Core Functions
  • Movie Handling
    • movie
    • load()
    • load_movie_chain()
  • Timeseries Handling
    • timeseries
  • Motion Correction
    • MotionCorrect
  • Estimates
    • Estimates
  • Deconvolution
    • constrained_foopsi()
    • constrained_oasisAR2()
  • Parameter Setting
    • CNMFParams
  • CNMF
    • CNMF
    • load_CNMF()
  • Online CNMF (OnACID)
    • OnACID
    • load_OnlineCNMF()
  • Preprocessing
    • preprocess_data()
  • Initialization
    • initialize_components()
    • greedyROI()
    • greedyROI_corr()
    • graphNMF()
    • sparseNMF()
  • Spatial Components
    • update_spatial_components()
  • Temporal Components
    • update_temporal_components()
  • Merge components
    • merge_components()
  • Utilities
    • detrend_df_f()
    • update_order()
    • get_file_size()
  • ROIs
    • register_ROIs()
    • register_multisession()
    • com()
    • extract_binary_masks_from_structural_channel()
  • Memory mapping
    • load_memmap()
    • save_memmap_join()
    • save_memmap()
  • Image statistics
    • local_correlations()
    • max_correlation_image()
    • correlation_pnr()
  • Parallel Processing functions
    • apply_to_patch()
    • start_server()
    • stop_server()
  • Ring-CNN functions
    • Masked_Conv2D
    • Hadamard
    • Additive
    • create_LN_model()
    • fit_NL_model()
    • quantile_loss()
  • VolPy
    • VOLPY
    • volparams
    • volspike()