aind-ephys-preprocessing/code/params.json at 1bbc0cc6e24029add46ef7a3e3c699e44da9fea1 · AllenNeuralDynamics/aind-ephys-preprocessing · GitHub

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{
    "job_kwargs": {
        "chunk_duration": "1s",
        "progress_bar": false,
        "mp_context": "spawn"
    },
    "min_preprocessing_duration": 120,
    "custom_preprocessing_pipeline": null,
    "denoising_strategy": "cmr",
    "filter_type": "highpass",
    "highpass_filter": {
        "freq_min": 300.0,
        "margin_ms": 5.0
    },
    "bandpass_filter": {
        "freq_min": 300.0,
        "freq_max": 6000.0,
        "margin_ms": 5.0
    },
    "phase_shift": {
        "margin_ms": 100.0
    },
    "detect_bad_channels": {
        "method": "coherence+psd",
        "dead_channel_threshold": -0.5,
        "noisy_channel_threshold": 1.0,
        "outside_channel_threshold": -0.3,
        "outside_channels_location": "top",
        "n_neighbors": 11,
        "seed": 0
    },
    "remove_out_channels": true,
    "remove_bad_channels": true,
    "max_bad_channel_fraction": 0.5,
    "common_reference": {
        "reference": "global",
        "operator": "median"
    },
    "highpass_spatial_filter": {
        "n_channel_pad": 60,
        "n_channel_taper": null,
        "direction": "y",
        "apply_agc": true,
        "agc_window_length_s": 0.01,
        "highpass_butter_order": 3,
        "highpass_butter_wn": 0.01
    },
    "motion_correction": {
        "preset": "dredge_fast",
        "detect_kwargs": {},
        "select_kwargs": {},
        "localize_peaks_kwargs": {},
        "estimate_motion_kwargs": {
            "win_step_norm": 0.1,
            "win_scale_norm": 0.1
        },
        "interpolate_motion_kwargs": {}
    }
}