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1. Fernandez-Ruiz 2017 PV vs SST metrics 2. Adjust processing code so doesn't require waveforms to be run 3. Calculate CCG and transmission probability in 20s bins 4. Runners for my project & Kei's paper
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| function cell_metrics = FR2017(cell_metrics,session,spikes,parameters) | ||
| % This is an example template for creating your own calculations | ||
| % | ||
| % INPUTS | ||
| % cell_metrics - cell_metrics struct | ||
| % session - session struct with session-level metadata | ||
| % spikes_intervalsExcluded - spikes struct filtered by (manipulation) intervals | ||
| % spikes - spikes cell struct | ||
| % spikes{1} : all spikes | ||
| % spikes{2} : spikes excluding manipulation intervals | ||
| % parameters - input parameters to ProcessCellExplorer | ||
| % | ||
| % OUTPUT | ||
| % cell_metrics - updated cell_metrics struct | ||
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| sr = session.extracellular.sr; | ||
| spikes = spikes{1}; | ||
| if any(spikes.total==0) | ||
| cell_indexes = find(spikes.total>0); | ||
| else | ||
| cell_indexes = 1:spikes.numcells; | ||
| end | ||
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| % acg_mean = nan(1,spikes.numcells); | ||
| burst_index = nan(1,spikes.numcells); | ||
| refrac = nan(1,spikes.numcells); | ||
| for i = cell_indexes | ||
| acg = CCG(spikes.times{i},ones(size(spikes.times{i})),'binSize',0.001,'duration',.1,'norm','rate','Fs',1/sr); | ||
| acg = acg(51:end); % subset to after spike | ||
| % acg_mean(i) = mean(acg); | ||
| if max(acg(1:10))==0 | ||
| burst_index(i) = 0; | ||
| else | ||
| burst_index(i) = (max(acg(1:10)) - mean(acg(end-10:end)))/max(acg(1:10)); | ||
| end | ||
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| [~, max_ind] = max(acg); | ||
| for m = 2:max_ind | ||
| slope(m) = (acg(m) - acg(1))/(m - 1); | ||
| end | ||
| slope_sd = std(slope); | ||
| exceed_1SD = find(slope > slope_sd); | ||
| refrac(i) = exceed_1SD(1) - 1; | ||
| end | ||
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| % cell_metrics.acg_mean_FR = acg_mean; | ||
| cell_metrics.burst_index_FR = burst_index; | ||
| cell_metrics.refrac_period_FR = refrac; | ||
| end |
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| @@ -0,0 +1,39 @@ | ||
| %% set session | ||
| animal = 'BaggySweatpants'; | ||
| session_name = '20220214_BaggySweatpants_DY01'; | ||
| basepath = ['Z:\WT_Sequences\2022_winter\Preprocessed_Data\Spikes\g1\',animal,'\Ecephys\',... | ||
| session_name,'\catgt_',session_name,'_g1\',session_name,'_g1_imec0']; | ||
| cd(basepath) | ||
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| %% calculate | ||
| tic | ||
| % % set params | ||
| session = sessionTemplate(basepath); | ||
| session.extracellular.fileName = [session_name,'_g1_tcat.imec0.ap.bin']; | ||
| session.extracellular.srLfp = 2500; | ||
| % session = gui_session(session); | ||
| % validateSessionStruct(session); | ||
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| % generate metrics file | ||
| cell_metrics = ProcessCellMetrics('session', session,... | ||
| 'metrics',{'monoSynaptic_connections'},... | ||
| 'includeInhibitoryConnections',true,... | ||
| 'manualAdjustMonoSyn',false,... | ||
| 'getWaveformsFromDat',false,... | ||
| 'showWaveforms',false,... | ||
| 'sessionSummaryFigure',false,... | ||
| 'showGUI',false); | ||
| toc | ||
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| % %% view | ||
| % cell_metrics = CellExplorer('metrics',cell_metrics); | ||
| % | ||
| % %% view from file | ||
| % animal = 'BaggySweatpants'; | ||
| % session_name = '20220214_BaggySweatpants_DY01'; | ||
| % basepath = ['Z:\WT_Sequences\2022_winter\Preprocessed_Data\Spikes\g1\',animal,'\Ecephys\',... | ||
| % session_name,'\catgt_',session_name,'_g1\',session_name,'_g1_imec0']; | ||
| % cd(basepath) | ||
| % session = loadSession; | ||
| % cell_metrics = loadCellMetrics; | ||
| % cell_metrics = CellExplorer('metrics',cell_metrics); |
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| addpath(genpath("C:\Users\Niflheim\Documents\GitHub\External\CellExplorer")) | ||
| % set session | ||
| basepath = "\\oak-smb-giocomo.stanford.edu\groups\giocomo\export\data\Projects\JohnKei_NPH3"; | ||
| load('\\oak-smb-giocomo.stanford.edu\groups\giocomo\fkmasuda\fkm_analysis\EAJ_revisions\wt_ket_sessions.mat') | ||
| for s = 1:length(wt_ket_sessions) | ||
| datadir = sprintf('%s\\%s\\%s_keicontrasttrack_ketamine1_g0\\%s_keicontrasttrack_ketamine1_g0_imec0',... | ||
| basepath,wt_ket_sessions{s,1},wt_ket_sessions{s,2},wt_ket_sessions{s,2}); | ||
| cd(datadir) | ||
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| % set params | ||
| session = sessionTemplate(datadir); | ||
| session.extracellular.fileName = [wt_ket_sessions{s,2},'_keicontrasttrack_ketamine1_g0_t0.imec0.ap.bin']; | ||
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| % generate metrics file | ||
| cell_metrics = ProcessCellMetrics('session', session,... | ||
| 'metrics',{'monoSynaptic_connections'},... | ||
| 'includeInhibitoryConnections',true,... | ||
| 'manualAdjustMonoSyn',false,... | ||
| 'getWaveformsFromDat',false,... | ||
| 'showWaveforms',false,... | ||
| 'sessionSummaryFigure',false,... | ||
| 'showGUI',false); | ||
| end |