CaImAn documentation

Contents:

• Overview
  • Companion paper
  • Questions, comments, issues
  • License
• Caiman 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
• Installation and Updating
  • Section 1: Install Caiman
    • Section 1A. Install with conda
    • Section 1B. Development-mode install
  • Section 2: Set up demos with caimanmanager
  • Section 3: Upgrading
    • Section 3A: Upgrade conda install
    • Section 3B: Upgrade the dev-mode install
    • Section 3C: Upgrade the demos with caimanmanager
  • Section 4: Miscellaneous
    • Section 4A: System Requirements
    • Section 4B: Installing additional packages
    • Section 4C: Setting up environment variables
    • Section 4D: Other topics
• Getting Started
  • 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
  • Logging
  • Estimator design
  • Cluster setup and shutdown
  • Memory Mapping
• Handling movies
  • Loading movies
  • Saving movies
  • Visualizing movies
  • Manipulating movies
    • concatenation
    • movie resizing
• Performance Guide
  • Online versus offline
  • Clustering options
  • Patch size
  • Alternate builds of dependencies and unsupported environment variables
• General Tips
  • Motion Correction tips
  • Caiman Online Processing tips
  • Caiman Batch processing tips
  • 1p processing tips
  • Deconvolution tips
• File Formats
  • Matlab (*.mat)
  • TIFF (*.tiff, *.tif, *.btf)
  • AVI/MKV (*.avi, *.mkv)
  • Numpy arrays (*.npy, *.npz)
  • HDF5/N5/zarr (*.h5, *.hdf5, *.n5, *.zarr)
  • Memmapped Numpy Array (*.mmap)
  • Scanbox Format (*.sbx)
  • SIMA (*.sima)
  • Zipfile full of images (*.zip)
• File Formats: Addenda
  • Conversion tools
  • Adding new types
• Graphical interfaces
  • The Caiman GUI
  • External interfaces
• CaImAn and GPUs
  • Caiman and CUDA
  • Installation
  • Use
• On Clustering
  • Ipyparallel vs multiprocessing
  • How to select one with the codebase
  • Issues
• Core Functions
  • Movie Handling
    • movie
    • movie.play()
    • movie.resize()
    • movie.computeDFF()
    • get_file_size()
    • load()
    • load_iter()
    • load_movie_chain()
  • Timeseries Handling
    • timeseries
    • timeseries.save()
  • Motion Correction
    • MotionCorrect
    • MotionCorrect.motion_correct()
    • MotionCorrect.motion_correct_rigid()
    • MotionCorrect.motion_correct_pwrigid()
    • MotionCorrect.apply_shifts_movie()
    • motion_correct_oneP_rigid()
    • motion_correct_oneP_nonrigid()
  • Estimates
    • Estimates
    • Estimates.compute_residuals()
    • Estimates.deconvolve()
    • Estimates.detrend_df_f()
    • Estimates.evaluate_components()
    • Estimates.evaluate_components_CNN()
    • Estimates.filter_components()
    • Estimates.hv_view_components()
    • Estimates.nb_view_components()
    • Estimates.nb_view_components_3d()
    • Estimates.normalize_components()
    • Estimates.play_movie()
    • Estimates.plot_contours()
    • Estimates.plot_contours_nb()
    • Estimates.remove_duplicates()
    • Estimates.remove_small_large_neurons()
    • Estimates.select_components()
    • Estimates.restore_discarded_components()
    • Estimates.save_NWB()
    • Estimates.view_components()
  • Deconvolution
    • constrained_foopsi()
    • constrained_oasisAR2()
  • Parameter Setting
    • CNMFParams
    • CNMFParams.__init__()
    • CNMFParams.set()
    • CNMFParams.get()
    • CNMFParams.get_group()
    • CNMFParams.change_params()
    • CNMFParams.to_dict()
  • CNMF
    • CNMF
    • CNMF.fit()
    • CNMF.refit()
    • CNMF.fit_file()
    • CNMF.save()
    • CNMF.deconvolve()
    • CNMF.update_spatial()
    • CNMF.update_temporal()
    • CNMF.compute_residuals()
    • CNMF.remove_components()
    • CNMF.HALS4traces()
    • CNMF.HALS4footprints()
    • CNMF.merge_comps()
    • CNMF.initialize()
    • CNMF.preprocess()
    • load_CNMF()
  • Online CNMF (OnACID)
    • OnACID
    • OnACID.fit_online()
    • OnACID.fit_next()
    • OnACID.save()
    • OnACID.initialize_online()
    • 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()
  • 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
    • setup_cluster()
    • start_server()
    • stop_server()
  • Ring-CNN functions
    • Masked_Conv2D
    • Hadamard
    • Additive
    • create_LN_model()
    • fit_NL_model()
    • quantile_loss()
  • VolPy
    • VOLPY
    • VOLPY.__init__()
    • VOLPY.fit()
    • volparams
    • volparams.__init__()
    • volparams.set()
    • volparams.get()
    • volparams.get_group()
    • volparams.change_params()
    • volspike()