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curation_machine_learning_models

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added metrics parameters

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  1. model_info.json +158 -0
model_info.json ADDED
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+ {
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+ "metric_params": {
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+
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+ "quality_metric_params": {
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+ "metric_names": [
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+ "num_spikes",
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+ "firing_rate",
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+ "presence_ratio",
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+ "snr",
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+ "isi_violation",
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+ "rp_violation",
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+ "sliding_rp_violation",
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+ "amplitude_cutoff",
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+ "amplitude_median",
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+ "amplitude_cv",
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+ "synchrony",
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+ "firing_range",
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+ "drift",
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+ "isolation_distance",
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+ "l_ratio",
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+ "d_prime",
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+ "nearest_neighbor",
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+ "silhouette"
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+ ],
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+ "sparsity": null,
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+ "peak_sign": null,
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+ "seed": null,
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+ "qm_params": {
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+ "presence_ratio": {
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+ "bin_duration_s": 60,
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+ "mean_fr_ratio_thresh": 0.0
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+ },
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+ "snr": {
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+ "peak_sign": "neg",
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+ "peak_mode": "extremum",
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+ "random_chunk_kwargs_dict": null
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+ },
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+ "isi_violation": {
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+ "isi_threshold_ms": 1.5,
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+ "min_isi_ms": 0
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+ },
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+ "rp_violation": {
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+ "refractory_period_ms": 1.0,
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+ "censored_period_ms": 0.0
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+ },
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+ "sliding_rp_violation": {
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+ "min_spikes": 0,
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+ "bin_size_ms": 0.25,
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+ "window_size_s": 1,
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+ "exclude_ref_period_below_ms": 0.5,
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+ "max_ref_period_ms": 10,
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+ "contamination_values": null
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+ },
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+ "synchrony": {
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+ "synchrony_sizes": [
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+ 2,
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+ 4,
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+ 8
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+ ]
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+ },
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+ "firing_range": {
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+ "bin_size_s": 5,
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+ "percentiles": [
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+ 5,
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+ 95
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+ ]
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+ },
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+ "amplitude_cv": {
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+ "average_num_spikes_per_bin": 50,
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+ "percentiles": [
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+ 5,
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+ 95
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+ ],
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+ "min_num_bins": 10,
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+ "amplitude_extension": "spike_amplitudes"
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+ },
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+ "amplitude_cutoff": {
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+ "peak_sign": "neg",
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+ "num_histogram_bins": 100,
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+ "histogram_smoothing_value": 3,
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+ "amplitudes_bins_min_ratio": 5
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+ },
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+ "amplitude_median": {
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+ "peak_sign": "neg"
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+ },
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+ "drift": {
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+ "interval_s": 60,
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+ "min_spikes_per_interval": 100,
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+ "direction": "y",
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+ "min_num_bins": 2
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+ },
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+ "nearest_neighbor": {
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+ "max_spikes": 10000,
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+ "n_neighbors": 5
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+ },
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+ "nn_isolation": {
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+ "max_spikes": 10000,
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+ "min_spikes": 10,
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+ "min_fr": 0.0,
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+ "n_neighbors": 4,
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+ "n_components": 10,
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+ "radius_um": 100,
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+ "peak_sign": "neg"
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+ },
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+ "nn_noise_overlap": {
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+ "max_spikes": 10000,
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+ "min_spikes": 10,
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+ "min_fr": 0.0,
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+ "n_neighbors": 4,
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+ "n_components": 10,
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+ "radius_um": 100,
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+ "peak_sign": "neg"
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+ },
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+ "silhouette": {
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+ "method": [
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+ "simplified"
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+ ]
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+ }
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+ },
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+ "skip_pc_metrics": false
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+ },
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+ "template_metric_params": {
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+ [
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+ "half_width",
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+ "num_negative_peaks",
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+ "num_positive_peaks",
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+ "peak_to_valley",
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+ "peak_trough_ratio",
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+ "recovery_slope",
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+ "repolarization_slope"
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+ ],
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+ "sparsity": null,
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+ "peak_sign": "neg",
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+ "upsampling_factor": 10,
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+ "metrics_kwargs": {
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+ "recovery_window_ms": 0.7,
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+ "peak_relative_threshold": 0.2,
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+ "peak_width_ms": 0.1,
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+ "depth_direction": "y",
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+ "min_channels_for_velocity": 5,
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+ "min_r2_velocity": 0.5,
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+ "exp_peak_function": "ptp",
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+ "min_r2_exp_decay": 0.5,
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+ "spread_threshold": 0.2,
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+ "spread_smooth_um": 20,
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+ }
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+ }
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+
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+ },
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+ "spikeinterface_info": {
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+ "version": "0.100.0"
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+ },
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+ "label_conversion": {
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+ "accept": "accept",
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+ "reject": "accept"
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+ }
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+
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+ }