CaImAn Source Extraction¶

Overview¶

The CaImAn source extraction tool is used to perform automated source extraction from calcium imaging movies using the CNMF/CNMF-E algorithm¹ offered in the open-source package CaImAn². The algorithm aims to retrieve the spatial location and temporal dynamics of individual neurons.

Inputs¶

The workflow supports individual movies and movie series. When a movie series is provided, the movies are concatenated temporally and analyzed as a single movie. When a movie series is processed, the number of output files will match the number of input files. For instance, for each input movie file, a corresponding output cell set file will be generated. While all output cell set files will contain the same spatial footprints, the temporal activity stored in each cell set file will match the timeline of the corresponding input movie.

Once the input movie is selected, an optional parameter file may be selected and used to override the parameters specified in the analysis table. The input files and processing parameters are listed in the table below.

Parameters¶

Optional Parameters File Format¶

A json file may be uploaded to IDEAS and used to specify CaImAn's processing parameters. To override the analysis table parameters with the parameters specified in the json file supplied, the Overwrite Analysis Table Parameters parameter must be set to True. Sample parameter files from CaImAn are included below for reference.

Sample Parameters File

source_extraction_parameters.json (additional example json files can be found in CaImAn's repository)

{
    "data": {
        "fr": 10,
        "decay_time": 0.4
    },
    "init": {
        "method_init": "corr_pnr",
        "K": null,
        "gSig": [3, 3],
        "gSiz": [13, 13],
        "ssub": 1,
        "tsub": 2,
        "nb": 0,
        "min_corr": 0.6,
        "min_pnr": 7,
        "normalize_init": false,
        "center_psf": true,
        "ssub_B": 2,
        "ring_size_factor": 1.4
    },
    "preprocess": {
        "p": 1
    },
    "temporal": {
        "p": 1,
        "method_deconvolution": "oasis"
    },
    "spatial": {
        "update_background_components": true
    },
    "patch": {
        "rf": 40,
        "stride": 20,
        "only_init": true,
        "nb_patch": 0,
        "low_rank_background": null,
        "del_duplicates": true
    },
    "merging": {
        "merge_thr": 0.7
    }
}

1P vs 2P Data Processing¶

The workflow is compatible with both 1P and 2P data. The parameters that control the initialization step as well as how to model background fluctuations can be adjusted based on the input data. The default parameters are set for processing 1P data. The table below summarizes the parameters that may be adjusted based on the desired workflow. None means the parameter is unspecified and the corresponding analysis table cell is left empty. Note that K must be set based on the expected number of components per patch for 2P data.

Outputs¶

The workflow will produce the outputs listed below.

CaImAn Output¶

hdf5 file containing the model and data produced by CaImAn. This includes the model itself and the results of the algorithm, including cellular footprints, temporal dynamics, spikes, noise estimates, background activity, residuals, and more.

The data preview includes the initialization images used by the algorithm as well as the spatial footprints and raw temporal traces of putative cells detected by CaImAn.

Raw Cell Set(s)¶

isxd cell set(s) containing the spatial footprints and raw temporal traces of the cells identified by CaImAn.

Denoised Cell Set(s)¶

isxd cell set(s) containing the spatial footprints and denoised temporal traces of the cells identified by CaImAn.

Spike Event Set(s)¶

isxd event set(s) containing the neural events identified by CaImAn.