########################## # SpikeDetekt parameters # ########################## experiment_name = 'AFR1_140103' raw_data_files =['AFRtriple1_030114-2_linear1_reo.dat', 'AFRtriple1_030114_cage_awake_reo.dat', 'AFRtriple1_030114_cage_awake2_reo.dat', 'AFRtriple1_030114-2_cage_reo.dat', 'AFRtriple1_030114_cage1_reo.dat'] prb_file = 'AFR1_reorder.prb' nbits = 16 voltage_gain = 400 sample_rate = 20000 nchannels = 64 # Filtering # --------- filter_low = 500. # Low pass frequency (Hz) filter_high = 0.95 * .5 * sample_rate filter_butter_order = 3 # Order of Butterworth filter. filter_lfp_low = 0 # LFP filter low-pass frequency filter_lfp_high = 300 # LFP filter high-pass frequency save_raw = False # only true for speding future runs of SpikeDetekt save_high = False save_low = False # Chunks # ------ chunk_size = int(1. * sample_rate) # 1 second chunk_overlap = int(.015 * sample_rate) # 15 ms # Spike detection # --------------- # Uniformly scattered chunks, for computing the threshold from the std of the # signal across the whole recording. nexcerpts = 50 excerpt_size = int(1. * sample_rate) threshold_strong_std_factor = 7 threshold_weak_std_factor = 3. detect_spikes = 'negative' precomputed_threshold = None #features_contiguous = 0 # Connected component # ------------------- connected_component_join_size = int(.00005 * sample_rate) # Spike extraction # ---------------- extract_s_before = 16 extract_s_after = 16 waveforms_nsamples = extract_s_before + extract_s_after # Features # -------- nfeatures_per_channel = 3 # Number of features per channel. pca_nwaveforms_max = 10000 ######################### # KlustaKwik parameters # ######################### KK_MaskStarts = 100 # TEST what is better KK_MaxPossibleClusters = 200 # TEST what is better KK_MaxIter = 10000 # if reduced it finish soon but maybe less quality clusters KK_RandomSeed = 654 KK_SplitFirst = 20 KK_SplitEvery = 90 # default is 40, as higher as less splitting time KK_Subset = 1 # set to 50-100 for test on a subset of the data KK_UseDistributional = 1 # set to 0 for unmasked clustering #KK_RamLimitGB = -1 # uncoment to desactivate RAM limit KK_UseMaskedInitialConditions = 1 # don't understad this, default is 0 KK_AssignToFirstClosestMask = 1 # don't understad this, default is 0 ### Same as default KK_SaveSorted = 0 KK_PenaltyK = 0 KK_PenaltyKLogN = 1 KK_FullStepEvery = 20 # don't understad this #MinClusters = 100 # those params are for unmasked mode only #MaxClusters = 110