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Merged
lkaraba merged 2 commits into from
Mar 12, 2026
Merged

Barr updates #21

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76700ce
small updates to BARR detector
lkaraba Mar 12, 2026
21c969f
labeling update
lkaraba Mar 12, 2026
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10 changes: 5 additions & 5 deletions BARRs/BARR_PSTH.m
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Original file line number Diff line number Diff line change
Expand Up @@ -225,9 +225,9 @@ function BARR_PSTH(plotSave,useState)
if plotRips
% PSTH_ripples = computePSTH(ripples,spikes,'duration',1,'plots', false,'alignment','peaks','zscorePlot',false);
% [PSTH_ripples,PSTH_t] = makePETH(spikes,ripples.timestamps(:,1),[-3 3]);
[PSTH_ripples, PSTH_t] = manualPSTH(spikes, ripples.timestamps(:,1),[-1,1],1/1000);
[PSTH_ripples, PSTH_t] = manualPSTH(spikes, ripples.timestamps(:,1),[-1,1],1/100); %was 1/1000
if runTags
warning('NOT ADJUSTED TO NEW DIMENSIONS');
%warning('NOT ADJUSTED TO NEW DIMENSIONS');
% for k = 1:size(PSTH_ripples,1)
% if ((max(PSTH_ripples(k,91:111))-max(PSTH_ripples(k,1:71))) > 1.5*std(PSTH_ripples(k,:)))
% cell_metrics.tags.Pr = [cell_metrics.tags.Pr spikes.UID(k)];
Expand All @@ -248,9 +248,9 @@ function BARR_PSTH(plotSave,useState)
end
% PSTH_bar = computePSTH(HSEnrem,spikes,'duration',1,'plots', false,'alignment','peaks','zscorePlot',false);
% [PSTH_bar,PSTH_t] = makePETH(spikes,HSEuse.timestamps(:,1),[-3 3]);
[PSTH_bar, PSTH_t] = manualPSTH(spikes, HSEuse.timestamps(:,1),[-1 1],1/1000);
[PSTH_bar, PSTH_t] = manualPSTH(spikes, HSEuse.timestamps(:,1),[-1 1],1/100); %was 1/1000
if runTags
warning('NOT ADJUSTED TO NEW DIMENSIONS');
%warning('NOT ADJUSTED TO NEW DIMENSIONS');
% for k = 1:size(PSTH_bar,1)
% if (mean(PSTH_bar(k,1001:2001))-mean(PSTH_bar(k,1:100))) > 0.3
% cell_metrics.tags.Pb = [cell_metrics.tags.Pb spikes.UID(k)];
Expand Down Expand Up @@ -414,7 +414,7 @@ function BARR_PSTH(plotSave,useState)
shuffled_r = cumsum([shuffled_iri]); %raly had cumsum([0; shuffled_iri]);

[ccg_ripple_barrage_shuf,t_ripple_barrage_shuf] = CCG(cat(1,shuffled_r,t_barrages{1}),cat(1,t_ripple_id{1},2*t_barrage_id{1}),'binSize',binsize,'duration',duration,'norm','rate');
figure(5);plot(t_ripple_barrage_shuf,ccg_ripple_barrage_shuf(:,2,1),'r');hold on;title('ccg barr-SWR'); yline(0,'k--');xlim([-3 3]);
figure(5);plot(t_ripple_barrage_shuf,ccg_ripple_barrage_shuf(:,2,1),'r');hold on;title('ccg barr-SWR shuffle'); yline(0,'k--');xlim([-3 3]);
saveas(gcf,[plotSave 'CCG_shuff.png']);
% Old jitter start
% for it = 1:10000
Expand Down
22 changes: 16 additions & 6 deletions BARRs/detectBARR.m
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Expand Up @@ -53,12 +53,14 @@
% Default: 0
% pareDur: Minimum duration of BARRs kept, in seconds. This should
% generally be kept at or below 0.2. Default: 0.2
% zeroRip: Logical option to zero firing during SWRs. This is
% typically used for sessions containing stimulation (ie
% ripple generation). This seems to be a better option than
% remRip.Default: false
% remRip: Logical option to remove BARRs which overlap with ripples.
% zeroRip: Logical option to remove BARRs which overlap with ripples.
% This seems to be a better option than remRip.
% Default: false
% remRip: Logical option to zero firing during SWRs. This is
% typically used for sessions containing stimulation (ie
% ripple generation). Default: false
% newSpks: Logical option to regenerate spike groups if the regions or
% cell types have been adjusted. Default: false
%
%%%%%%%%%%%%%%%
%%% OUTPUTS %%%
Expand Down Expand Up @@ -101,6 +103,7 @@
addParameter(p, 'pareDur', 0.2, @isnumeric);
addParameter(p, 'zeroRip', true, @islogical);
addParameter(p, 'remRip', false, @islogical);
addParameter(p, 'newSpks', false, @islogical);

parse(p, varargin{:});

Expand All @@ -118,6 +121,7 @@
pareDur = p.Results.pareDur;
zeroRip = p.Results.zeroRip;
remRip = p.Results.remRip;
newSpks = p.Results.newSpks;

%% Check if BARRs have already been detected
basename = basenameFromBasepath(basepath);
Expand All @@ -135,7 +139,7 @@
mkdir([basepath filesep 'Barrage_Files']);
end

pullSpikes('basepath', basepath, 'savePath', [basepath filesep 'Barrage_Files'], 'force', true); %Get region/cell type spike files
pullSpikes('basepath', basepath, 'savePath', [basepath filesep 'Barrage_Files'], 'force', newSpks); %Get region/cell type spike files

if ~exist(strcat(basepath,filesep,'Barrage_Files',filesep,basename,'.CA2pyr.cellinfo.mat'))
disp('No CA2 pyramidal cells detected, exiting');
Expand Down Expand Up @@ -174,6 +178,12 @@
'recordMetrics',true,'remRip',remRip);

HSE = pareBARRs(basepath, HSE, spikes, savePath, unMin, spkNum, pareDur, spkHz, zeroRip, unMax);
%add unitsForDetection parameters
HSE.detectorinfo.Hz = Hz;
HSE.detectorinfo.ft = ft;
HSE.detectorinfo.numEvt = numEvt;
HSE.detectorinfo.savePath = savePath;
save([savePath 'HSE.mat'], 'HSE');

%% Save NeuroScope2 file
BARR_N2(basepath);
Expand Down
9 changes: 9 additions & 0 deletions BARRs/pareBARRs.m
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Original file line number Diff line number Diff line change
Expand Up @@ -136,5 +136,14 @@
HSE.fin = HSE.keep(HSE.NREM(HSE.nonRip));
disp(['Final num: ' num2str(length(HSE.fin))]);
disp(['Num removed: ' num2str(length(HSE.NREM) - length(HSE.fin))]);

%%add parameters
HSE.detectorinfo.numCell = numCell;
HSE.detectorinfo.numSpk = numSpk;
HSE.detectorinfo.pareDur = pareDur;
HSE.detectorinfo.singleHz = singleHz;
HSE.detectorinfo.stim = stim;
HSE.detectorinfo.maxCell = maxCell;

save([savePath 'HSE.mat'], 'HSE');
end
5 changes: 3 additions & 2 deletions BARRs/pullSpikes.m
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Expand Up @@ -16,7 +16,7 @@ function pullSpikes(varargin)
addParameter(p,'savePath',pwd,@ischar);
addParameter(p,'force',false,@islogical);

parse(p,varargin{:})
parse(p, varargin{:});

basepath = p.Results.basepath;
savePath = p.Results.savePath;
Expand All @@ -27,8 +27,8 @@ function pullSpikes(varargin)
basename = basenameFromBasepath(basepath);

%% Remove old runs if necessary
getFiles = dir();
if force
getFiles = dir();
fun_existsPyr = @(x) (contains(x, 'pyr.cellinfo.mat'));
fun_existsInt = @(x) (contains(x, 'int.cellinfo.mat'));
toDelete = zeros(size(getFiles,1),1);
Expand All @@ -53,6 +53,7 @@ function pullSpikes(varargin)
fun_existsInt = @(x) (contains(x, 'int.cellinfo.mat'));
for j = 1:size(getFiles,1)
if fun_existsPyr(getFiles(j).name)||fun_existsInt(getFiles(j).name)
cd(original);
disp('Region spike structures detected, returning');
return
end
Expand Down
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