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+### Note that depending on the file format selected, the parameters in the data section can vary
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+### You should refer to the documentation to know what are the needed parameters for a given
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+### file format. Otherwise, launch the code and a message will tell you what is needed
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+
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+[data]
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+file_format = numpy # Can be raw_binary, openephys, hdf5, ... See >> spyking-circus help -i for more info
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+sampling_rate = 32000.0
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+stream_mode = None # None by default. Can be multi-files, or anything depending to the file format
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+mapping = /net/bs-filesvr01/export/group/hierlemann/Temp/Alessio/make_test_sorted_data/sorting_output/spykingcircus/probe.prb # Mapping of the electrode (see http://spyking-circus.rtfd.ord)
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+suffix = # Suffix to add to generated files
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+global_tmp = True # should be False if local /tmp/ has enough space (better for clusters)
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+overwrite = True # Filter or remove artefacts on site (if write access is possible). Data are duplicated otherwise
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+parallel_hdf5 = True # Use the parallel HDF5 feature (if available)
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+
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+[detection]
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+radius = auto # Radius [in um] (if auto, read from the prb file)
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+N_t = 3 # Width of the templates [in ms]
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+spike_thresh = 6 # Threshold for spike detection
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+peaks = negative # Can be negative (default), positive or both
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+
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+[filtering]
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+cut_off = 300, auto # Min and Max (auto=nyquist) cut off frequencies for the band pass butterworth filter [Hz]
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+filter = True # If True, then a low-pass filtering is performed
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+remove_median = False # If True, median over all channels is substracted to each channels (movement artifacts)
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+
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+[triggers]
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+trig_file = # External stimuli to be considered as putative artefacts [in trig units] (see documentation)
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+trig_windows = # The time windows of those external stimuli [in trig units]
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+trig_unit = ms # The unit in which times are expressed: can be ms or timestep
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+clean_artefact = False # If True, external artefacts induced by triggers will be suppressed from data
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+dead_file = # Portion of the signals that should be excluded from the analysis [in dead units]
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+dead_unit = ms # The unit in which times for dead regions are expressed: can be ms or timestep
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+ignore_times = False # If True, any spike in the dead regions will be ignored by the analysis
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+make_plots = # Generate sanity plots of the averaged artefacts [Nothing or None if no plots]
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+
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+[whitening]
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+spatial = True # Perform spatial whitening
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+max_elts = 1000 # Max number of events per electrode (should be compatible with nb_elts)
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+nb_elts = 0.8 # Fraction of max_elts that should be obtained per electrode [0-1]
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+output_dim = 5 # Can be in percent of variance explain, or num of dimensions for PCA on waveforms
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+
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+[clustering]
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+extraction = median-raw # Can be either median-raw (default) or mean-raw
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+sub_dim = 10 # Number of dimensions to keep for local PCA per electrode
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+max_elts = 10000 # Max number of events per electrode (should be compatible with nb_elts)
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+nb_elts = 0.8 # Fraction of max_elts that should be obtained per electrode [0-1]
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+nb_repeats = 3 # Number of passes used for the clustering
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+smart_search = True # Activate the smart search mode
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+merging_method = nd-bhatta # Method to perform local merges (distance, dip, folding, nd-folding, bhatta, nd-bhatta)
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+merging_param = default # Merging parameter (see doc) (3 if distance, 0.5 if dip, 1e-3 if folding, 2 if bhatta)
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+sensitivity = 3 # Single parameter for clustering sensitivity. The lower the more sensitive
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+cc_merge = 0.95 # If CC between two templates is higher, they are merged
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+dispersion = (5, 5) # Min and Max dispersion allowed for amplitudes [in MAD]
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+make_plots = # Generate sanity plots of the clustering [Nothing or None if no plots]
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+
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+[fitting]
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+amp_limits = (0.3, 5) # Amplitudes for the templates during spike detection [if not auto] (0.3, 5)
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+amp_auto = True # True if amplitudes are adjusted automatically for every templates
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+collect_all = False # If True, one garbage template per electrode is created, to store unfitted spikes
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+ratio_thresh = 0.9 # Ratio of the spike_threshold used while fitting [0-1]. The lower the slower
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+
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+[merging]
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+cc_overlap = 0.75 # Only templates with CC higher than cc_overlap may be merged
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+cc_bin = 2 # Bin size for computing CC [in ms]
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+default_lag = 5 # Default length of the period to compute dip in the CC [ms]
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+auto_mode = 0.75 # Between 0 (aggressive) and 1 (no merging). If empty, GUI is launched
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+remove_noise = True # If True, meta merging will remove obvious noise templates (weak amplitudes)
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+noise_limit = 0.75 # Amplitude at which templates are classified as noise
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+sparsity_limit = 0 # Sparsity level (in percentage) for selecting templates as putative noise (in [0, 1])
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+time_rpv = 5 # Time [in ms] to consider for Refraction Period Violations (RPV) (0 to disable)
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+rpv_threshold = 0.02 # Percentage of RPV allowed while merging
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+merge_drifts = True # Try to automatically merge drifts, i.e. non overlapping spiking neurons
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+drift_limit = 1 # Distance for drifts. The higher, the more non-overlapping the activities should be
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+
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+[converting]
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+erase_all = True # If False, a prompt will ask you to export if export has already been done
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+export_pcs = prompt # Can be prompt [default] or in none, all, some
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+export_all = False # If True, unfitted spikes will be exported as the last Ne templates
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+sparse_export = False # For recent versions of phy, and large number of templates/channels
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+
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+[validating]
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+nearest_elec = auto # Validation channel (e.g. electrode closest to the ground truth cell)
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+max_iter = 200 # Maximum number of iterations of the stochastic gradient descent (SGD)
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+learning_rate = 1.0e-3 # Initial learning rate which controls the step-size of the SGD
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+roc_sampling = 10 # Number of points to estimate the ROC curve of the BEER estimate
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+test_size = 0.3 # Portion of the dataset to include in the test split
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+radius_factor = 0.5 # Radius factor to modulate physical radius during validation
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+juxta_dtype = uint16 # Type of the juxtacellular data
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+juxta_thresh = 6 # Threshold for juxtacellular detection
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+juxta_valley = False # True if juxta-cellular spikes are negative peaks
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+juxta_spikes = # If none, spikes are automatically detected based on juxta_thresh
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+filter = True # If the juxta channel need to be filtered or not
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+make_plots = png # Generate sanity plots of the validation [Nothing or None if no plots]
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+
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+[extracting]
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+safety_time = 1 # Temporal zone around which spikes are isolated [in ms]
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+max_elts = 1000 # Max number of collected events per templates
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+output_dim = 5 # Percentage of variance explained while performing PCA
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+cc_merge = 0.975 # If CC between two templates is higher, they are merged
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+noise_thr = 0.8 # Minimal amplitudes are such than amp*min(templates) < noise_thr*threshold
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+
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+[noedits]
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+filter_done = True #!! AUTOMATICALLY EDITED: DO NOT MODIFY !!
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+artefacts_done = False # Will become True automatically after removing artefacts
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+median_done = False # Will become True automatically after removing common median
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