### Note that depending on the file format selected, the parameters in the data section can vary ### You should refer to the documentation to know what are the needed parameters for a given ### file format. Otherwise, launch the code and a message will tell you what is needed [data] file_format = raw_binary # Can be raw_binary, openephys, hdf5, ... See >> spyking-circus help -i for more info sampling_rate = 20000 data_dtype = int16 nb_channels = 64 gain = 1 data_offset = 0 dtype_offset = auto stream_mode = None # None by default. Can be multi-files, or anything depending to the file format mapping = NeuroNexus_6shank_64Ch.prb # Mapping of the electrode (see http://spyking-circus.rtfd.ord) suffix = # Suffix to add to generated files global_tmp = True # should be False if local /tmp/ has enough space (better for clusters) overwrite = True # Filter or remove artefacts on site (if write access is possible). Data are duplicated otherwise [detection] radius = auto # Radius [in um] (if auto, read from the prb file) N_t = 1.5 # Width of the templates [in ms] spike_thresh = 5.5 # Threshold for spike detection peaks = negative # Can be negative (default), positive or both matched-filter = False # If True, we perform spike detection with matched filters matched_thresh = 5 # Threshold for detection if matched filter is True alignment = True # Realign the waveforms by oversampling [filtering] cut_off = 300, 8000 # Min and Max (auto=nyquist) cut off frequencies for the band pass butterworth filter [Hz] filter = True # If True, then a low-pass filtering is performed remove_median = True # If True, median over all channels is substracted to each channels (movement artifacts) [triggers] trig_file = # If external stimuli need to be considered as putative artefacts (see documentation) trig_windows = # The time windows of those external stimuli [in ms] clean_artefact = False # If True, external artefacts induced by triggers will be suppressed from data make_plots = # Generate sanity plots of the averaged artefacts [Nothing or None if no plots] [whitening] chunk_size = 30 # Size of the data chunks [in s] safety_time = 1 # Temporal zone around which templates are isolated [in ms, or auto] temporal = False # Perform temporal whitening spatial = True # Perform spatial whitening max_elts = 10000 # Max number of events per electrode (should be compatible with nb_elts) nb_elts = 0.8 # Fraction of max_elts that should be obtained per electrode [0-1] output_dim = 5 # Can be in percent of variance explain, or num of dimensions for PCA on waveforms [clustering] extraction = median-raw # Can be either median-raw (default), median-pca, mean-pca, mean-raw safety_space = True # If True, we exclude spikes in the vicinity of a selected spikes safety_time = auto # Temporal zone around which templates are isolated [in ms, or auto] max_elts = 40000 # Max number of events per electrode (should be compatible with nb_elts) nb_elts = 0.8 # Fraction of max_elts that should be obtained per electrode [0-1] nclus_min = 0.005 # Min number of elements in a cluster (given in percentage) [0-1] max_clusters = 30 # Maximal number of clusters for every electrodes nb_repeats = 3 # Number of passes used for the clustering smart_search = True # Parameter to activate the smart search mode sim_same_elec = 3 # Distance within clusters under which they are re-merged compress = True # Compress templates for large physical radius or number of electrodes cc_merge = 0.975 # If CC between two templates is higher, they are merged dispersion = (5, 5) # Min and Max dispersion allowed for amplitudes [in MAD] noise_thr = 0.8 # Minimal amplitudes are such than amp*min(templates) < noise_thr*threshold in [0-1] remove_mixture = True # At the end of the clustering, we remove mixtures of templates make_plots = # Generate sanity plots of the clustering [Nothing or None if no plots] [fitting] chunk_size = 1 # Size of chunks used during fitting [in second] gpu_only = False # Use GPU for computation of b's AND fitting [not optimized yet] amp_limits = (0.3, 5) # Amplitudes for the templates during spike detection [if not auto] amp_auto = True # True if amplitudes are adjusted automatically for every templates max_chunk = inf # Fit only up to max_chunk collect_all = False # If True, one garbage template per electrode is created, to store unfitted spikes [merging] cc_overlap = 0.5 # Only templates with CC higher than cc_overlap may be merged cc_bin = 2 # Bin size for computing CC [in ms] correct_lag = True # If spikes are aligned when merging. May be better for phy usage [converting] erase_all = True # If False, a prompt will ask you to export if export has already been done export_pcs = all # Can be prompt [default] or in none, all, some export_all = False # If True, unfitted spikes will be exported as the last Ne templates [validating] nearest_elec = auto # Validation channel (e.g. electrode closest to the ground truth cell) max_iter = 200 # Maximum number of iterations of the stochastic gradient descent (SGD) learning_rate = 1.0e-3 # Initial learning rate which controls the step-size of the SGD roc_sampling = 10 # Number of points to estimate the ROC curve of the BEER estimate test_size = 0.3 # Portion of the dataset to include in the test split radius_factor = 0.5 # Radius factor to modulate physical radius during validation juxta_dtype = uint16 # Type of the juxtacellular data juxta_thresh = 6 # Threshold for juxtacellular detection juxta_valley = False # True if juxta-cellular spikes are negative peaks make_plots = png # Generate sanity plots of the validation [Nothing or None if no plots] [extracting] safety_time = 1 # Temporal zone around which spikes are isolated [in ms] max_elts = 1000 # Max number of collected events per templates output_dim = 5 # Percentage of variance explained while performing PCA cc_merge = 0.975 # If CC between two templates is higher, they are merged noise_thr = 0.8 # Minimal amplitudes are such than amp*min(templates) < noise_thr*threshold [noedits] filter_done = True #!! AUTOMATICALLY EDITED: DO NOT MODIFY !! artefacts_done = False # Will become True automatically after removing artefacts median_done = True #!! AUTOMATICALLY EDITED: DO NOT MODIFY !!