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v3.1.0
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Bugfix: raw waveform display fixed for the manual GUI.
  Waveforms did not display if you used an older .prm file
'fir1' filter is supported for "vcFilter" parameter.
  Finite Impulse Response filter
  The frequency range is sett by "freqLim=[f_low, f_high]" parameter.
New default: Detection threshold set to "qqFactor = 5".
  Increasing the detection threshold can incorrectly merge large amplitude units with background noise.
New default: Auto-calculation of maxSite and nSites_ref based on the physical distance.
  maxSite=[] and nSites_ref=[] will automatically set it based on the site spacing and layout.
  The parameter "maxDist_site_um" is used to determine the number of sites used for features (default 50 um)
  The parameter "maxDist_site_spk_um" is used to determine the number of reference sites (default 75 um)
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@jamesjun
jamesjun committed Oct 26, 2017
1 parent 48dee16 commit 78117ab
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13 changes: 13 additions & 0 deletions change_log.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,19 @@
J. James Jun

--------------------------------------------------------------------
[2017/10/26: v3.1.0]
Bugfix: raw waveform display fixed for the manual GUI.
Waveforms did not display if you used an older .prm file
'fir1' filter is supported for "vcFilter" parameter.
Finite Impulse Response filter
The frequency range is sett by "freqLim=[f_low, f_high]" parameter.
New default: Detection threshold set to "qqFactor = 5".
Increasing the detection threshold can incorrectly merge large amplitude units with background noise.
New default: Auto-calculation of maxSite and nSites_ref based on the physical distance.
maxSite=[] and nSites_ref=[] will automatically set it based on the site spacing and layout.
The parameter "maxDist_site_um" is used to determine the number of sites used for features (default 50 um)
The parameter "maxDist_site_spk_um" is used to determine the number of reference sites (default 75 um)

[2017/10/25: v3.0.9]
Faster auto-splitting. Now displaying three principal component axis.
Individual spike waveforms are no longer displayed but mean waveforms are displayed
Expand Down
9 changes: 5 additions & 4 deletions default.prm
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ fInverse_file = 0; % flip polarity of set to one
header_offset = 0; % File header offset (set to 0 for files containing no header info (e.g. WHISPER format)

% #Execution parameters
version = 'v3.0.9'; % JRCLUST version. Updated on Oct 25, 2017
version = 'v3.1.0'; % JRCLUST version. Updated on Oct 26, 2017
fVerbose = 0;
fParfor = 1; % Use Multiple cores
fGpu = 1; % Use GPU
Expand Down Expand Up @@ -60,13 +60,13 @@ gain_boost = 1; % multiply the raw recording by this gain to boost u
thresh_corr_bad_site = []; % Automatically reject bad sites based on the max. correlation with neighboring sites using raw waveforms. Set to [] to disable

% #Spike detection and grouping (run "jrc spikesort" after change)
qqFactor = 4; % Spike detection thresold (Threshold = qqFactor*S, S = med(x-med(x))/.6745). (RQ Quiroga'04).
qqFactor = 5; % Spike detection thresold (Threshold = qqFactor*S, S = med(x-med(x))/.6745). (RQ Quiroga'04).
qqSample = 4; % Median subsample factor (1 every n)
spkThresh_uV = []; % Manual threshold (applies to all channels)
spkThresh_max_uV = []; % maximum absolute amp. allowed
spkLim_ms = [-.25, .75]; % Time range to capture the filtered spike waveforms
spkLim_raw_ms = []; % Raw spike waveform range, setting to [] will use spkLim_ms
maxSite = 6.5; % Max number of sites (nSpikes_spk = 1+2*maxSite-nSite_ref), nSpikes_spk*nFet_spk<=30
maxSite = []; % Max number of sites (nSpikes_spk = 1+2*maxSite-nSite_ref), nSpikes_spk*nFet_spk<=30
spkRefrac_ms = .25; % Detection refractory period
vcSpatialFilter = 'none'; % Spatial filter for detection {'mean', 'imec2', 'subtract', 'csd'}
fSaveEvt = 1; % Flag to save event file
Expand All @@ -76,11 +76,12 @@ blank_thresh = []; % reject spikes exceeding the channel mean after fil
blank_period_ms = 5; % (miliseconds) Duration of blanking when the common mean exceeds a threhold (blank_thresh)
nneigh_min_detect = 0; % Min. number of neighbors near the spike below threshold. choose between [0,1,2]
maxDist_site_um = 50; % Radius of spike event merging. Keep spikes that has most negative peaks within x um radius.
maxDist_site_spk_um = 70; % Max. radius for extracting waveforms. Used if maxSite=[] and nSites_ref=[]

% #Feature extraction (run "jrc spikesort" after change)
vcFet = 'gpca'; % Feature list: {'gpca', 'cov', 'spacetime', 'vpp', 'vmin', 'vminmax', 'energy', 'pca'}
nPcPerChan = 1; % number of principal components per chan.
nSites_ref = 4; % set to 0 for global referencing (move to feature section) @TODO: diagram
nSites_ref = []; % set to 0 for global referencing (move to feature section) @TODO: diagram
vcSpkRef = 'nmean'; % Subtract mean of the spiking event sites {'nmean', 'none'}

% #Clustering (run "jrc sort" after change)
Expand Down
142 changes: 105 additions & 37 deletions jrc3.m
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@
if strcmpi(vcCmd, 'makeprm-all'), jrc3('all', vcFile_prm_); end
case 'makeprm-f', makeprm_(vcArg1, vcArg2, 0, vcArg3);
case 'import-tsf', import_tsf_(vcArg1);
case 'import-h5', import_h5_(vcArg1);
case 'import-jrc1', import_jrc1_(vcArg1);
case 'export-jrc1', export_jrc1_(vcArg1);
case 'import-intan', vcFile_prm_ = import_intan_(vcArg1, vcArg2, vcArg3); return;
Expand Down Expand Up @@ -1073,7 +1074,7 @@ function detect_(P)
%--------------------------------------------------------------------------
function [nLoad1, nSamples_load1, nSamples_last1] = plan_load_(nBytes_file, P)
% plan load file size according to the available memory and file size (nBytes_file1)
LOAD_FACTOR = 10; %GPU memory usage factor. 4x means 1/4 of GPU memory can be loaded
LOAD_FACTOR = 5; %GPU memory usage factor. 4x means 1/4 of GPU memory can be loaded

nSamples1 = floor(nBytes_file / bytesPerSample_(P.vcDataType) / P.nChans);
% nSamples_max = floor(mem_max_(P) / P.nChans / 4); % Bound by MAX_BYTES_LOAD
Expand All @@ -1087,6 +1088,7 @@ function detect_(P)
end
nSamples_max = min(floor(P.MAX_BYTES_LOAD / P.nChans), floor(P.sRateHz * P.MAX_LOAD_SEC)); % 1 min window
elseif isempty(P.MAX_LOAD_SEC)
% if isempty(P.MAX_LOAD_SEC)
nSamples_max = floor(P.MAX_BYTES_LOAD / P.nChans / bytesPerSample_(P.vcDataType));
else
nSamples_max = floor(P.sRateHz * P.MAX_LOAD_SEC);
Expand Down Expand Up @@ -1208,46 +1210,45 @@ function detect_(P)

%--------------------------------------------------------------------------
function [P, vcFile_prm] = loadParam_(vcFile_prm, fEditFile)
% Load prm file

if nargin<2, fEditFile = 1; end
% Load prm file
if ~exist(vcFile_prm, 'file')
error('.prm file does not exist: %s\n', vcFile_prm);
% P=[]; return;
end
assert_(exist_file_(vcFile_prm), sprintf('.prm file does not exist: %s\n', vcFile_prm));
P0 = file2struct_(jrcpath_(read_cfg_('default_prm', 0))); %P = defaultParam();
P = file2struct_(vcFile_prm);
if ~isfield(P, 'template_file'), P.template_file = ''; end
if ~isempty(P.template_file)
P0 = struct_merge_(P0, file2struct_(P.template_file));
assert_(exist_file_(P.template_file), sprintf('template file does not exist: %s', P.template_file));
P = struct_merge_(file2struct_(P.template_file), P);
end
P.vcFile_prm = vcFile_prm;
% todo: substitute bin file path
assert(isfield(P, 'vcFile'), sprintf('Check "%s" file syntax', vcFile_prm));
assert_(isfield(P, 'vcFile'), sprintf('Check "%s" file syntax', vcFile_prm));

if ~exist(P.vcFile, 'file')
if ~exist_file_(P.vcFile)
P.vcFile = replacePath_(P.vcFile, vcFile_prm);
if ~exist(P.vcFile, 'file')
if ~exist_file_(P.vcFile)
fprintf('vcFile not specified. Assuming multi-file format ''csFiles_merge''.\n');
end
end


%-----
% Load prb file
if ~isfield(P, 'probe_file'), P.probe_file = P0.probe_file; end
try
probe_file_ = find_prb_(P.probe_file);
if isempty(probe_file_)
P.probe_file = replacePath_(P.probe_file, vcFile_prm);
if ~exist(P.probe_file, 'file'), error('prb file does not exist'); end
assert_(exist_file_(P.probe_file), 'prb file does not exist');
else
P.probe_file = probe_file_;
end
P0 = load_prb_(P.probe_file, P0);
catch
fprintf('loadParam: %s not found.\n', P.probe_file);
end

% Load prb file
P = struct_merge_(P0, P);
if isempty(get_(P, 'maxSite')), P = calc_maxSite_(P); end

% check GPU
P.fGpu = ifeq_(license('test', 'Distrib_Computing_Toolbox'), P.fGpu, 0);
Expand All @@ -1265,9 +1266,6 @@ function detect_(P)
P.spkLim = round(P.spkLim_ms * P.sRateHz / 1000);
P.spkLim_raw = round(get_set_(P, 'spkLim_raw_ms', P.spkLim_ms) * P.sRateHz / 1000); %10/17/2017 JJJ: changed from spkLim_wav*2

% if isempty(P.spkLim_ms_fet), P.spkLim_ms_fet = P.spkLim_ms; end
% P.spkLim_fet = round(P.spkLim_ms_fet * P.sRateHz / 1000);
% P.slopeLim = round(P.slopeLim_ms * P.sRateHz / 1000);
if isempty(get_(P, 'nDiff_filt'))
if isempty(get_(P, 'nDiff_ms_filt'))
P.nDiff_filt = 0;
Expand All @@ -1292,11 +1290,33 @@ function detect_(P)
if isempty(get_(P, 'vcFilter_show'))
P.vcFilter_show = P.vcFilter;
end
assert(validate_param_(P), 'Parameter file contains error.');
assert_(validate_param_(P), 'Parameter file contains error.');
if fEditFile, edit(P.vcFile_prm); end % Show settings file
end %func


%--------------------------------------------------------------------------
% 10/25/17 JJJ: Created and tested
function P = calc_maxSite_(P)
% Auto determine maxSite from the radius and site ifno

if ~isempty(get_(P, 'maxSite')), return; end
mrDist_site = pdist2(P.mrSiteXY, P.mrSiteXY);
maxDist_site_um = get_set_(P, 'maxDist_site_um', 50);
nSites_fet = median(sum(mrDist_site <= maxDist_site_um));
if isempty(get_(P, 'nSites_ref'))
maxDist_site_spk_um = get_set_(P, 'maxDist_site_spk_um', maxDist_site_um+25);
nSites_spk = median(sum(mrDist_site <= maxDist_site_spk_um));
P.maxSite = (nSites_spk-1)/2;
P.nSites_ref = nSites_spk - nSites_fet;
else
nSites_spk = nSites_fet + P.nSites_ref;
P.maxSite = (nSites_spk-1)/2;
end
fprintf('Auto-set: maxSite=%0.1f, nSites_ref=%0.1f\n', P.maxSite, P.nSites_ref);
end %func


%--------------------------------------------------------------------------
% 9/27/17 JJJ: Created and tested
function vcFilter = get_filter_(P)
Expand Down Expand Up @@ -2710,16 +2730,18 @@ function close_hFig_traces_(hFig, event)
switch lower(P.vcFilter)
case 'user'
% vnFilter_user = -[5,0,-3,-4,-3,0,5]; % sgdiff acceleration
vnFilter_user = int16(get_set_(P, 'vnFilter_user', []));
vnFilter_user = single(get_set_(P, 'vnFilter_user', []));
assert_(~isempty(vnFilter_user), 'Set vnFilter_user to use vcFilter=''user''');
for i=1:size(mnWav2,2)
mnWav2(:,i) = conv(mnWav2(:,i), vnFilter_user, 'same');
end
case 'fir1'
n5ms = round(P.sRateHz / 1000 * 5);
vrFilter = single(fir1(n5ms, P.freqLim/P.sRateHz*2));
for i=1:size(mnWav2,2)
mnWav2(:,i) = conv(mnWav2(:,i), vrFilter, 'same');
end
case 'ndiff'
% mnWav2(3:end-2,:) = (mnWav2(5:end,:)-mnWav2(3:end-2,:)) + (mnWav2(4:end-1,:)-mnWav2(2:end-3,:)); mnWav2([1,2,end-1,end],:) = 0;
% mnWav2(3:end-2,:) = 2*(mnWav2(4:end-1,:)-mnWav2(2:end-3,:)) + (mnWav2(5:end,:)-mnWav2(1:end-4,:)); mnWav2([1,2,end-1,end],:) = 0;
% mnWav2(3:end-2,:) = mnWav2(1:end-4,:) + mnWav2(2:end-3,:) + mnWav2(4:end-1,:) + mnWav2(5:end,:) - 4 * mnWav2(3:end-2,:);
% mnWav2(3:end-2,:) = -2*(mnWav2(1:end-4,:) - mnWav2(3:end-2,:) + mnWav2(5:end,:)) + mnWav2(2:end-3,:) + mnWav2(4:end-1,:); %2nd derivative, flip sign
mnWav2 = ndiff_(mnWav2, P.nDiff_filt);
case {'sgdiff', 'sgfilt'}
mnWav2 = sgfilt_(mnWav2, P.nDiff_filt);
Expand Down Expand Up @@ -3683,7 +3705,8 @@ function exit_manual_(src, event)
function vrX = wav_clu_x_(iClu, P)
% determine x range of a cluster
if P.fWav_raw_show
nSamples = diff(P.spkLim_raw) + 1;
dimm_raw = get0_('dimm_raw');
nSamples = dimm_raw(1); %diff(P.spkLim_raw) + 1;
x_offset = (P.spkLim_raw(2)) / nSamples + iClu - 1;
% vrX = (0:nSamples-1) / nSamples + x_offset;
else
Expand Down Expand Up @@ -4585,7 +4608,7 @@ function update_plot2_proj_(vrX, vrY)
function tnWav1 = tnWav1_sites_1_(tnWav1_, miSites1, viSites1)
[nT_spk, nSites_spk, nSpk1] = size(tnWav1_);
nSites1 = numel(viSites1);
% assert(nSites_spk==nSites1, 'tnWav1_sites_: nSites must agree');
% assert_(nSites_spk==nSites1, 'tnWav1_sites_: nSites must agree');
tnWav1 = zeros([nT_spk, nSpk1, nSites1], 'like', tnWav1_); %subset of spk, complete
for iSite1 = 1:nSites1
[viSite11, viiSpk11] = find(miSites1 == viSites1(iSite1));
Expand Down Expand Up @@ -4636,7 +4659,7 @@ function update_plot2_proj_(vrX, vrY)
% nSites1 = numel(viSites1);
nSites = numel(P.viSite2Chan);
tnWav1 = zeros([nT_spk, nSites, nSpk1], 'like', tnWav1_); %full
% assert(nSites_spk==nSites1, 'tnWav1_sites_: nSites must agree');
% assert_(nSites_spk==nSites1, 'tnWav1_sites_: nSites must agree');
% tnWav1 = zeros([nT_spk, nSpk1, nSites1], 'like', tnWav1_); %subset of spk, complete
for iSite1 = 1:numel(viSites1)
iSite11 = viSites1(iSite1);
Expand Down Expand Up @@ -5565,7 +5588,7 @@ function FigWavCor_update_(S0)
for iClu3 = iClu+1:S_clu.nClu % update cluster chain info
S_clu = S_clu_update_note_(S_clu, iClu3, get_next_clu_(S_clu, iClu3) - 1);
end
assert(S_clu_valid_(S_clu), 'Cluster number is inconsistent after deleting');
assert_(S_clu_valid_(S_clu), 'Cluster number is inconsistent after deleting');
end %func


Expand Down Expand Up @@ -5756,7 +5779,7 @@ function restore_clu_(varargin)
S_clu = S_clu_update_(S_clu, iClu1, P);
S_clu = delete_clu_(S_clu, iClu2);
% S_clu = S_clu_remove_empty_(S_clu);
assert(S_clu_valid_(S_clu), 'Cluster number is inconsistent after merging');
assert_(S_clu_valid_(S_clu), 'Cluster number is inconsistent after merging');
fprintf('%s [W] merging Clu %d and %d\n', datestr(now, 'HH:MM:SS'), iClu1, iClu2);
end %func

Expand Down Expand Up @@ -9438,7 +9461,7 @@ function plot_raster_clu_(viTime_clu, vrTime_trial, P, hAx)
viStart(viStart > viEnd(end)) = [];
nGroup = numel(viStart);
if nGroup==0, return; end
assert(nGroup == numel(viEnd), 'spike_refrac_:nStart==nEnd');
assert_(nGroup == numel(viEnd), 'spike_refrac_:nStart==nEnd');
vlRemove = false(size(viTime_spk));

for iGroup = 1:nGroup
Expand Down Expand Up @@ -12122,7 +12145,7 @@ function fig_traces_reset_(S_fig)
[vl, viA] = ismember(int32(viB), int32(viA2B));

% vl = ismember(viB, viA2B);
% assert(all(vl), 'reverse_lookup_: all viB must belong to viA2B');
% assert_(all(vl), 'reverse_lookup_: all viB must belong to viA2B');
% viA = arrayfun(@(i)find(viA2B==i), viB(vl), 'UniformOutput', 1);
end %func

Expand Down Expand Up @@ -12238,7 +12261,7 @@ function fig_traces_reset_(S_fig)
tnWav_spk_raw = gather_(tnWav_spk_raw);
nSite_use = P.maxSite*2+1 - P.nSites_ref;
if nSite_use==1, nFet_use=1; end
assert(nSite_use >0, 'nSites_use = maxSite*2+1 - nSites_ref must be greater than 0');
assert_(nSite_use >0, 'nSites_use = maxSite*2+1 - nSites_ref must be greater than 0');
switch nFet_use
case 3
[viSite2_spk, viSite3_spk] = find_site_spk23_(tnWav_spk, viSite_spk_, P); fprintf('.');
Expand Down Expand Up @@ -16227,7 +16250,7 @@ function export_prm_(vcFile_prm, vcFile_out_prm, fShow)
if isempty(vcTemplate_prm)
vcTemplate_prm = jrcpath_(read_cfg_('default_prm'));
end
assert(exist_file_(vcTemplate_prm), sprintf('Template file does not exist: %s', vcTemplate_prm));
assert_(exist_file_(vcTemplate_prm), sprintf('Template file does not exist: %s', vcTemplate_prm));

% Write to a .prm file
try
Expand Down Expand Up @@ -16528,8 +16551,8 @@ function plot_aux_rate_(fSelectedUnit)
% 9/29/17 JJJ: Displaying the version number of the program and what's used. #Tested
function [vcVer, vcDate, vcVer_used] = jrc_version_(vcFile_prm)
if nargin<1, vcFile_prm = ''; end
vcVer = 'v3.0.9';
vcDate = '10/25/2017';
vcVer = 'v3.1.0';
vcDate = '10/26/2017';
vcVer_used = '';
if nargout==0
fprintf('%s (%s) installed\n', vcVer, vcDate);
Expand Down Expand Up @@ -16788,7 +16811,7 @@ function edit_(vcFile)
if isempty(fid_)
[P, dimm_] = get0_('P', 'dimm_spk');
vcFile_ = strrep(P.vcFile_prm, '.prm', '_spkwav.jrc');
assert(exist_file_(vcFile_), sprintf('File must exist: %s\n', vcFile_));
assert_(exist_file_(vcFile_), sprintf('File must exist: %s\n', vcFile_));
fid_ = fopen(vcFile_, 'r');
end

Expand Down Expand Up @@ -16821,7 +16844,7 @@ function edit_(vcFile)
if isempty(fid_)
[P, dimm_] = get0_('P', 'dimm_raw');
vcFile_ = strrep(P.vcFile_prm, '.prm', '_spkraw.jrc');
assert(exist_file_(vcFile_), sprintf('File must exist: %s\n', vcFile_));
assert_(exist_file_(vcFile_), sprintf('File must exist: %s\n', vcFile_));
fid_ = fopen(vcFile_, 'r');
end

Expand Down Expand Up @@ -17191,4 +17214,49 @@ function assert_(flag, vcMsg)
errordlg(vcMsg);
disperr_(vcMsg);
end
end
end

%--------------------------------------------------------------------------
% 10/26/17 JJJ: Created
function import_h5_(vcFile_h5)
% Brian Allen h5 data
if nargin<1, vcFile_h5 = ''; end
if isempty(vcFile_h5), vcFile_h5 = 'E:\BrianAllen\915_18\915_18_1\915_18_1.h5'; end

S_h5.att.patch_sample_rate = h5readatt(vcFile_h5, '/', 'abfsamplerate');
S_h5.att.mea_sample_rate = h5readatt(vcFile_h5, '/', 'MEAsamplerate');
S_h5.att.probe_layout = h5readatt(vcFile_h5, '/','probelayout');
S_h5.att.bad_channels = h5readatt(vcFile_h5, '/','badchannels');
S_h5.att.n_chans = S_h5.att.probe_layout(1) * S_h5.att.probe_layout(2);
% S_h5.att.max_chan = h5readatt(vcFile_h5, '/', 'spikes'); %spikes/max_channel');
% S_h5.spikes.burst_index = h5read(vcFile_h5, '/spikes/burstindex');

%% CONSTANTS
% options.data_length = 30;
% options.data_length = Inf;
% % length of data to pull in, in seconds. Set to Inf if you wish to pull
% % in all the data at once (typically ~8 minutes worth)
% options.isi_criterion = .02; % 20ms, from Staba, Richard J., et al. "Single neuron..
% %burst firing in the human hippocampus during sleep." Hippocampus 12.6 (2002): 724-734.
% options.spike_wfm_len = .002; %plot 2ms on each side of spike peak
[vcDir, vcFile, vcExt] = fileparts(vcFile_h5);
vcFile_raw = fullfile(vcDir, 'Recordings', [vcFile, '_raw.h5']);
vcFile_filtered = fullfile(vcDir, 'Recordings', [vcFile, '_filtered.h5']);

rawMEA = h5read(vcFile_raw, '/rawMEA');
rawPipette = h5read(vcFile_raw, '/rawPipette');
syncMEA = h5read(vcFile_raw, '/syncMEA');

% if isinf(options.data_length)
data.mea = h5read(vcFile_h5, '/filtered/filteredMEA', [1 1], [Inf Inf]);
data.patch = h5read(vcFile_h5, '/raw/rawPipette', [1 1], [Inf 1]);
% else
% data.mea = h5read(filename, '/filtered/filteredMEA', [1 1], [(options.data_length * data.att.mea_sample_rate) Inf]);
% data.patch = h5read(filename, '/raw/rawPipette', [1 1], [(options.data_length * data.att.mea_sample_rate) 1]);
% end

% P.uV_per_bit = 1/10;
% mnWav = int16(S_h5.mea * 1/P.uV_per_bit)';
% write_bin(vcFile_bin, mnWav)

end %func
4 changes: 2 additions & 2 deletions prb/kampff128.prb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,5 +20,5 @@ sRateHz = 30000;
viSiteZero = [];
uV_per_bit = 0.195;
vcDataType = 'uint16';
maxSite = 4;
nSites_ref = 0;
%maxSite = 4;
%nSites_ref = 0;
4 changes: 2 additions & 2 deletions prb/sample.prb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,6 @@ pad = [12 12];
shank = ones(size(channels)); % Leave it empty if single shank

% Default prm
maxSite = 6.5; % Number of neighboring sites in each direction to extract spike waveforms
nSites_ref = 4; % Total number of reference sites to exclude for feature extraction
%maxSite = 6.5; % Number of neighboring sites in each direction to extract spike waveforms
%nSites_ref = 4; % Total number of reference sites to exclude for feature extraction
um_per_pix = 20; % Micrometers per center-to-center vertical site spacing

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