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ChangeLog
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## NOTE: "->" indicates changes to computation or parameters that affect results
-------------------------------------------------------------------------------------
2014-08-07 Eero Simoncelli <[email protected]>
-> changed params.amplitude.kderange from [0.3 1.1] to [0.3 1.0]
(should be less than 1.0)
* AmplitudeThresholdGUI: added buttons, colors (to identify
cells), spike counts, inf => eliminate cell
2014-08-05 Eero Simoncelli <[email protected]>
* Offset channels in all displays
* spikesort_demo/cbp_spikesort_demo_script.m:
- Fixed bug: CBP step 2, recalculation of waveforms, was operating
on all spikes, not thresholded spikes.
2014-07-30 Eero Simoncelli <[email protected]>
* spikesort_demo/load_raw_data.m:
-> Changed default waveform_len for Harris data set from 81 to 35.
* spikesort_demo/preproc/OrderWaveformsByNorm.m
Modified order of waveforms: was originally sorted from smallest
to largest norm. Now reversed (largest to smallest).
* spikesort_demo/preproc/PartitionSignal.m (PartitionSignal):
Changed back to original thresholding rule:
params.partition.silence_threshold*std(rms)
2014-07-23 Eero Simoncelli <[email protected]>
* spikesort_demo/load_default_parameters.m:
set default filter.freq to [100 5000]
added cbp.lambda, cbp.reweight_exp, cbp.reweight_fn
* spikesort_demo/cbp_spikesort_demo_script.m:
added display of CBP recovered spikes, histograms of residual
errors, PC scatterplot
2014-07-21 Eero Simoncelli <[email protected]>
* spikesort_demo/load_default_parameters.m:
Eliminated params.whitening.p_norm parameter, which was not being used
-> Changed default params.partition.silence_threshold parameter from 3 to 4
* spikesort_demo/load_raw_data.m:
-> Changed default filtering cutoff for Harris data set from 800Hz to 400Hz
2014-07-18 Eero Simoncelli <[email protected]>
* spikesort_demo/load_default_parameters.m:
removed params.cbp.num_features. Unnecessary - can get it from length(init_features)
* spikesort_demo/SpikesortCBP.m:
Added waveforms argument to this function, and removed the cbp_outer.init_features parameter
* spikesort_demo/preproc/plotting/VisualizeClustering.m:
indicate centroids in scatter plot
display of waveforms/traces for multi-electrodes offset
match color scheme in clustering scatter and waveform plots
use same y-axis scaling for all waveforms
* spikesort_demo/preproc/EstimateInitialWaveforms.m (peak_idx):
princomp is being discontinued. Switched to call pca
-> don't re-center (subtract mean) when doing PCA
make waveform_len odd
* spikesort_demo/preproc/FilterData.m (data):
added histograms of raw data
2014-07-17 Peter Li
* put another Harris dataset into the example_data directory
* re-activated greedy solution for speedup
2014-07-16 Eero Simoncelli <[email protected]>
* spikesort_demo/preproc/PartitionSignal.m (signal_rms):
fixed bug introduced yesterday when changing parameterization...
2014-07-15 Eero Simoncelli <[email protected]>
* spikesort_demo/preproc/plotting/VisualizeClustering.m:
got rid of the second fignum argument (always make them consecutive)
added threshold argument
* spikesort_demo/preproc/PartitionSignal.m (snippet_centers):
partition.threshold -> partition.silence_threshold
partition.min_separation_len -> partition.min_silence_len
* spikesort_demo/preproc/EstimateInitialWaveforms.m (threshold):
-> Changed to just use threshold as is (compared directly to rms over channels);
* spikesort_demo/load_default_parameters.m:
-> clustering.threshold -> clustering.spike_threshold, value changed to 6
2014-07-14 Eero Simoncelli <[email protected]>
* spikesort_demo/spikesort_demo_setup.m:
Switched matlabpool calls to use parpool (matlabpool is being discontinued)
* spikesort_demo/cbp_spikesort_demo_script.m (params):
Moved plotting code into functions LoadRawData, FilterData, and PreprocessTrace
2014-07-06 Eero Simoncelli <[email protected]>
* spikesort_demo/load_default_parameters.m (adjust_wfsize_fn):
Moved cbp and cbp_outer parameters into here.
* spikesort_demo/preproc/PartitionSignal.m (dead_zone_idx):
Modified threshold code: threshold parameter is now in units of stdev.
* spikesort_demo/preproc/PreprocessTrace.m (noise_zone_idx):
- commented out display of pre-whitened marginal histograms.
These are not relevant, since we currently hardwire the exponent
to 2 in the CBP optimization.
* spikesort_demo/load_default_parameters.m:
- Moved num_waveforms back into clustering section (hadn't realized
there was a separate one for CBP!)
- Moved default partitioning parameters into here.
2014-07-05 Eero Simoncelli <[email protected]>
* spikesort_demo/load_raw_data.m:
-> Changed default Quiroga filtering.freq back to []
Current results on Quiroga dataset 1, with waveforms re-fit twice,
and threshold of cell 1 slightly hand-adjusted to eliminate
refractory violations:
Spike counts: [1921;1473;1138]
Clustering: Misses=241/3477 (6.93%) FPs=1531/4767 (32.12%)
CBP: Misses=3/3477 (0.09%) FPs=2/3476 (0.06%)
2014-07-03 Eero Simoncelli <[email protected]>
* spikesort_demo/spikesort_demo_setup.m:
error-protected the call to matlabpool, so that it now just gives
a warning.
* spikesort_demo/preproc/PreprocessTrace.m (noise_zone_idx):
noise_threshold parameter moved from general to whitening section.
* spikesort_demo/load_raw_data.m:
- re-organized loading of data files and specialization of
parameters. Now it's all done in this single function, which
replaces load_data_defaults.m
* spikesort_demo/load_default_parameters.m:
added plotting.first_fig_num, and changed all display code to use
figure numbers offset from this number
default fontsize changed to 12
num_waveforms parameter moved from clustering to general section
* spikesort_demo/preproc/plotting/VisualizeClustering.m (nh):
plot noise ball
* spikesort_demo/preproc/EstimateInitialWaveforms.m (threshold):
-> changed threshold for choosing segments for clustering to
mean + 4*std of a chi distribution (about 3.9)
* ToDo and ChangeLog: moved to main directory
* spikesort_demo/preproc/PreprocessTrace.m (nchan):
only plot cross-corr for multi-channel recordings
Display: fig3: histogram of norms, with threshold
fig4: ACF of noise regions
fig5: cross-channel correlations, but only if more than one channel!
fig6: noise distribution, compared with Gaussian and Laplacian
2014-07-02 Eero Simoncelli <[email protected]>
* cbp_spikesort_demo_script.m:
- moved top-level description text into README.md file. Added ecos
citation, and brief outline of algorithm.
- fixed bug: reweight_exp - this used to be hardcoded to three
entries
- further cleanup in plotting of histograms of filtered data
2014-07-01 Eero Simoncelli <[email protected]>
* load_data_defaults.m:
-> added 100Hz cutoff to Quiroga dataset
* cbp_spikesort_demo_script.m (dataMag):
- indicate filtering cutoffs in frequency plot
- plot chi2 distribution for comparison to data magnitude
* preproc/FilterData.m (Wn): allow params.filtering.freq to have a
single entry (low-freq cutoff) for a high-pass filter.
2014-06-19 Eero Simoncelli <[email protected]>
* preproc/PreprocessTrace:
- moved mean subtraction, and global rescaling operations into FilterData.m
- got rid of optional argument parsing for handling plot options, and used params.plotting.calibration_mode instead
2014-06-12 Eero Simoncelli <[email protected]>
* cbp_spikesort_demo_script:
- rewrote comments to describe algorithm steps
- added diagnotistic figures for filtering / whitening
- added plots of Fourier magnitudes
- added comments indicating what to verify in plots, and how to adjust parameters if needed
* load_default_parameters:
- added general.calibration_mode
* preproc/FilterData
- pad_size -> pad
- freq_range -> freq
Peter's results on Quiroga data
Spike counts: [1150;1187;1135]
Elapsed time is 71.133004 seconds.
Clust Misses=256/3477 (7.36 percent) FPs=4/3225 (0.12 percent)
CBP Misses=13/3477 (0.37 percent) FPs=2/3466 (0.06 percent)