noisy spikes in phy

[Fukuaki Kinoshita]

Dear Pierre, 

Thank you for your support always.

I have seen the results in the phy and found that spikes like noise are detected in the Traceview (attached file). I think that it is due to noisy templates.

How could I get appropriate templates and spikes?

I analyzed the data recorded for 30 min in 420 electrodes (electrode interval: 35um)

parameters in the params file are as below.

[data]
file_format    =raw_binary # openephys, hdf5, ... See >> spyking-circus help -i for more info
sampling_rate = 10000
data_dtype    = int16
nb_channels   = 420
stream_mode    = multi-files       # None by default. Can be multi-files, or anything depending to the file format
mapping        = probes/map_desyn400d2_20_r.prb # Mapping of the electrode (see http://spyking-circus.rtfd.org)
suffix         =            # Suffix to add to generated files, if needed
overwrite      = True       # Filter or remove artefacts on site (if write access is possible). Data are duplicated otherwise
parallel_hdf5  = True       # Use the parallel HDF5 feature (if available)
output_dir     =            # By default, generated data are in the same folder as the data.

[detection]
radius         = auto       # Radius [in um] (if auto, read from the prb file)
N_t            = 3          # Width of the templates [in ms]
spike_thresh   = 6.0          # Threshold [in MAD] for spike detection
peaks          = negative   # Can be negative (default), positive or both
dead_channels  =            # If not empty or specified in the probe, a dictionary 
weird_thresh   =            # If not empty, threshold [in MAD] for artefact detection

[filtering]
cut_off        = 300, auto  # 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  = False      # If True, medians over all channels within shanks are substracted (movement artifacts)
common_ground  =            # If you want to use channels as ground within shanks {channel_group : ground_channel}
sat_value      =          # Values higher than sat_value are set to 0 during filtering (in % of max dtype) [0,1]

[whitening]
spatial        = True       # Perform spatial whitening
max_elts       = 5000       # 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) or mean-raw
sub_dim        = 5         # Number of dimensions to keep for local PCA per electrode
max_elts       = 5000      # 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]
nb_repeats     = 5          # Number of passes used for the clustering
smart_search   = True       # Activate the smart search mode
merging_method = nd-bhatta  # Method to perform local merges (distance, dip, folding, nd-folding, bhatta, nd-bhatta)
merging_param  = default    # Merging parameter (see docs) (3 if distance, 0.5 if dip, 1e-9 if folding, 2 if bhatta)
sensitivity    = 3          # Single parameter for clustering sensitivity. The lower the more sensitive
cc_merge       = 0.98       # If CC between two templates is higher, they are merged
dispersion     = (2, 3)     # Min and Max dispersion allowed for amplitudes [in MAD]
fine_amplitude = True       # Optimize the amplitudes and compute a purity index for each template
make_plots     =   png         # Generate sanity plots of the clustering [Nothing or None if no plots]

[fitting]
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
collect_all    = False      # If True, one garbage template per electrode is created, to store unfitted spikes
ratio_thresh   = 0.9        # Ratio of the spike_threshold used while fitting [0-1]. The lower the slower
mse_error      = True      # If True, RMS is collected over time, to assess quality of reconstruction

[merging]
erase_all      = True       # If False, a prompt will ask you to remerge if merged has already been done
cc_overlap     = 0.98       # Only templates with CC higher than cc_overlap may be merged
cc_bin         = 2          # Bin size for computing CC [in ms]
default_lag    = 5          # Default length of the period to compute dip in the CC [ms]
auto_mode      = 0.90       # Between 0 (aggressive) and 1 (no merging). If empty, GUI is launched
remove_noise   = True       # If True, meta merging will remove obvious noise templates (weak amplitudes)
noise_limit    = 0.75       # Amplitude at which templates are classified as noise
sparsity_limit = 0.5          # Sparsity level (in percentage) for selecting templates as putative noise (in [0,1])
time_rpv       = 5          # Time [in ms] to consider for Refraction Period Violations (RPV) (0 to disable)
rpv_threshold  = 0.02       # Percentage of RPV allowed while merging
merge_drifts   = True       # Try to automatically merge drifts, i.e. non overlapping spiking neurons
drift_limit    = 1          # Distance for drifts. The higher, the more non-overlapping the activities should be
clean_merging  = True      # When templates are merged, automatically remove spike duplicated (less than 0.5ms appart)

Best Regards, 

Fukuaki K