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@luiztauffer
luiztauffer committed Jan 5, 2024
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Showing 1 changed file with 75 additions and 33 deletions.
108 changes: 75 additions & 33 deletions si_kilosort25/spec.json
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}
],
"parameters": [
{
"name": "lazy_read_input",
"description": "Lazy read input file",
"type": "bool",
"default": true
},
{
"name": "stub_test",
"description": "Stub test",
"type": "bool",
"default": false
},
{
"name": "recording_context.electrical_series_path",
"description": "Path to the electrical series in the NWB file",
"type": "str"
},
{
"name": "run_preprocessing",
"description": "Run preprocessing",
"type": "bool",
"default": true
},
{
"name": "preprocessing_context.preprocessing_strategy",
"description": "Strategy for preprocessing",
"type": "str",
"default": "cmr"
},
{
"name": "preprocessing_context.highpass_filter.freq_min",
"description": "Minimum frequency for the highpass filter",
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"default": 0.01
},
{
"name": "preprocessing_context.preprocessing_strategy",
"description": "Strategy for preprocessing",
"name": "preprocessing_context.motion_correction.compute",
"description": "Whether to compute motion correction",
"type": "bool",
"default": true
},
{
"name": "preprocessing_context.motion_correction.apply",
"description": "Whether to apply motion correction",
"type": "bool",
"default": false
},
{
"name": "preprocessing_context.motion_correction.preset",
"description": "Preset for motion correction",
"type": "str",
"default": "cmr"
"default": "nonrigid_accurate"
},
{
"name": "preprocessing_context.remove_out_channels",
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"default": 1.1
},
{
"name": "sorting_context.sorter_name",
"name": "run_spikesorting",
"description": "Run spike sorting",
"type": "bool",
"default": true
},
{
"name": "spikesorting_context.sorter_name",
"description": "Name of the sorter to use.",
"type": "str",
"default": "kilosort2_5"
},
{
"name": "sorting_context.sorter_kwargs.detect_threshold",
"name": "spikesorting_context.sorter_kwargs.detect_threshold",
"description": "Threshold for spike detection",
"type": "float",
"default": 6
},
{
"name": "sorting_context.sorter_kwargs.projection_threshold",
"name": "spikesorting_context.sorter_kwargs.projection_threshold",
"description": "Threshold on projections",
"type": "List[int]",
"default": [
Expand All @@ -181,112 +223,112 @@
]
},
{
"name": "sorting_context.sorter_kwargs.preclust_threshold",
"name": "spikesorting_context.sorter_kwargs.preclust_threshold",
"description": "Threshold crossings for pre-clustering (in PCA projection space)",
"type": "float",
"default": 8
},
{
"name": "sorting_context.sorter_kwargs.car",
"name": "spikesorting_context.sorter_kwargs.car",
"description": "Enable or disable common reference",
"type": "bool",
"default": true
},
{
"name": "sorting_context.sorter_kwargs.minFR",
"name": "spikesorting_context.sorter_kwargs.minFR",
"description": "Minimum spike rate (Hz), if a cluster falls below this for too long it gets removed",
"type": "float",
"default": 0.1
},
{
"name": "sorting_context.sorter_kwargs.minfr_goodchannels",
"name": "spikesorting_context.sorter_kwargs.minfr_goodchannels",
"description": "Minimum firing rate on a 'good' channel",
"type": "float",
"default": 0.1
},
{
"name": "sorting_context.sorter_kwargs.nblocks",
"name": "spikesorting_context.sorter_kwargs.nblocks",
"description": "blocks for registration. 0 turns it off, 1 does rigid registration. Replaces 'datashift' option.",
"type": "int",
"default": 5
},
{
"name": "sorting_context.sorter_kwargs.sig",
"name": "spikesorting_context.sorter_kwargs.sig",
"description": "spatial smoothness constant for registration",
"type": "float",
"default": 20
},
{
"name": "sorting_context.sorter_kwargs.freq_min",
"name": "spikesorting_context.sorter_kwargs.freq_min",
"description": "High-pass filter cutoff frequency",
"type": "float",
"default": 150
},
{
"name": "sorting_context.sorter_kwargs.sigmaMask",
"name": "spikesorting_context.sorter_kwargs.sigmaMask",
"description": "Spatial constant in um for computing residual variance of spike",
"type": "float",
"default": 30
},
{
"name": "sorting_context.sorter_kwargs.nPCs",
"name": "spikesorting_context.sorter_kwargs.lam",
"description": "The importance of the amplitude penalty (like in Kilosort1: 0 means not used, 10 is average, 50 is a lot)",
"type": "float",
"default": 10.0
},
{
"name": "spikesorting_context.sorter_kwargs.nPCs",
"description": "Number of PCA dimensions",
"type": "int",
"default": 3
},
{
"name": "sorting_context.sorter_kwargs.ntbuff",
"name": "spikesorting_context.sorter_kwargs.ntbuff",
"description": "Samples of symmetrical buffer for whitening and spike detection",
"type": "int",
"default": 64
},
{
"name": "sorting_context.sorter_kwargs.nfilt_factor",
"name": "spikesorting_context.sorter_kwargs.nfilt_factor",
"description": "Max number of clusters per good channel (even temporary ones) 4",
"type": "int",
"default": 4
},
{
"name": "sorting_context.sorter_kwargs.NT",
"description": "Batch size (if -1 it is automatically computed)",
"type": "int",
"default": -1
},
{
"name": "sorting_context.sorter_kwargs.AUCsplit",
"name": "spikesorting_context.sorter_kwargs.AUCsplit",
"description": "Threshold on the area under the curve (AUC) criterion for performing a split in the final step",
"type": "float",
"default": 0.9
},
{
"name": "sorting_context.sorter_kwargs.do_correction",
"name": "spikesorting_context.sorter_kwargs.do_correction",
"description": "If True drift registration is applied",
"type": "bool",
"default": true
},
{
"name": "sorting_context.sorter_kwargs.wave_length",
"name": "spikesorting_context.sorter_kwargs.wave_length",
"description": "size of the waveform extracted around each detected peak, (Default 61, maximum 81)",
"type": "float",
"default": 61
},
{
"name": "sorting_context.sorter_kwargs.keep_good_only",
"name": "spikesorting_context.sorter_kwargs.keep_good_only",
"description": "If True only 'good' units are returned",
"type": "bool",
"default": true
"default": false
},
{
"name": "sorting_context.sorter_kwargs.skip_kilosort_preprocessing",
"name": "spikesorting_context.sorter_kwargs.skip_kilosort_preprocessing",
"description": "Can optionaly skip the internal kilosort preprocessing",
"type": "bool",
"default": false
},
{
"name": "sorting_context.sorter_kwargs.scaleproc",
"description": "int16 scaling of whitened data, if -1 set to 200.",
"type": "int",
"default": -1
"name": "run_postprocessing",
"description": "Run postprocessing",
"type": "bool",
"default": true
}
],
"attributes": [
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