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- %% Figure 1
- load('Total Unit Information.mat');
- %% Firugre 1D
- % % ****** Flag of finding # of cells for specific condition ****** % %
- MeanFR=0.25;
- iHP = DepthFromCortex_iHP < 5.5;
- vHP = DepthFromCortex_iHP >= 5.5;
- main_dHP_exp = strcmp(SessionType_dHP,'SS') | strcmp(SessionType_dHP,'SSCH1') | strcmp(SessionType_dHP,'SSCH2') | strcmp(SessionType_dHP,'FRCH1') |...
- strcmp(SessionType_dHP,'FRCH2') | strcmp(SessionType_dHP,'SSFR1') | strcmp(SessionType_dHP,'SSFR2') | strcmp(SessionType_dHP,'T-SSCH1') |...
- strcmp(SessionType_dHP,'T-SSCH2') | strcmp(SessionType_dHP,'T-Quantity1') | strcmp(SessionType_dHP,'T-Quantity2');
- main_iHP_exp = strcmp(SessionType_iHP,'SS') | strcmp(SessionType_iHP,'SSCH1') | strcmp(SessionType_iHP,'SSCH2') | strcmp(SessionType_iHP,'FRCH1') |...
- strcmp(SessionType_iHP,'FRCH2') | strcmp(SessionType_iHP,'SSFR1') | strcmp(SessionType_iHP,'SSFR2') | strcmp(SessionType_iHP,'T-SSCH1') |...
- strcmp(SessionType_iHP,'T-SSCH2') | strcmp(SessionType_iHP,'T-Quantity1') | strcmp(SessionType_iHP,'T-Quantity2');
- %
- mask_dHP_LowIsolationQuality=(Assessment_dHP < 2);
- mask_dHP_HighIsolationQuality = ~mask_dHP_LowIsolationQuality;
- mask_dHP_LowStability=(NumberOfSpike_dHP(:,1)==0 | NumberOfSpike_dHP(:,4)==0) & mask_dHP_HighIsolationQuality;
- mask_dHP_HighStability = ~mask_dHP_LowStability;
- mask_dHP_GoodCluster=mask_dHP_HighStability & mask_dHP_HighIsolationQuality;
- mask_dHP_Interneuron = strcmp(Celltype_dHP,'Interneruon') & mask_dHP_HighStability & mask_dHP_HighIsolationQuality;
- mask_dHP_Pyramidal = strcmp(Celltype_dHP,'Pyramidal') & mask_dHP_HighStability & mask_dHP_HighIsolationQuality;
- mask_dHP_NonResponsive=(AvgFr_dHP(:,1) < MeanFR & AvgFr_dHP(:,2) < MeanFR & mask_dHP_HighIsolationQuality & mask_dHP_HighStability & mask_dHP_Pyramidal);
- mask_dHP_Responsive_Both=((AvgFr_dHP(:,1) >= MeanFR & AvgFr_dHP(:,2) >= MeanFR) & mask_dHP_HighIsolationQuality & mask_dHP_HighStability & mask_dHP_Pyramidal);
- mask_dHP_Responsive_OpenField=((AvgFr_dHP(:,1) >= MeanFR) & mask_dHP_HighIsolationQuality & mask_dHP_HighStability & mask_dHP_Pyramidal);
- mask_dHP_Responsive_RadialMaze=((AvgFr_dHP(:,2) >= MeanFR) & mask_dHP_HighIsolationQuality & mask_dHP_HighStability & mask_dHP_Pyramidal);
- LowScoreCLST.dHP=(Assessment_dHP(main_dHP_exp & mask_dHP_LowIsolationQuality));
- LowStabilityCLST.dHP=(Assessment_dHP(main_dHP_exp & mask_dHP_LowStability));
- AnalyzableCLST.dHP_INT=(Assessment_dHP(main_dHP_exp & mask_dHP_Interneuron));
- AnalyzableCLST.dHP_PYR=(Assessment_dHP(main_dHP_exp & mask_dHP_Pyramidal));
- AnalyzableCLST.dHP_PYR_NonResp=(Assessment_dHP(main_dHP_exp & mask_dHP_NonResponsive));
- AnalyzableCLST.dHP_PYR_Resp_Both=(Assessment_dHP(main_dHP_exp & mask_dHP_Responsive_Both));
- AnalyzableCLST.dHP_PYR_Resp_OpenField=(Assessment_dHP(main_dHP_exp & mask_dHP_Responsive_OpenField));
- AnalyzableCLST.dHP_PYR_Resp_RadialMaze=(Assessment_dHP(main_dHP_exp & mask_dHP_Responsive_RadialMaze));
- %
- mask_iHP_LowIsolationQuality=(Assessment_iHP < 2);
- mask_iHP_HighIsolationQuality = ~mask_iHP_LowIsolationQuality;
- mask_iHP_LowStability=(NumberOfSpike_iHP(:,1)==0 | NumberOfSpike_iHP(:,4)==0) & mask_iHP_HighIsolationQuality;
- mask_iHP_HighStability = ~mask_iHP_LowStability;
- mask_iHP_GoodCluster=mask_iHP_HighStability & mask_iHP_HighIsolationQuality;
- mask_iHP_Interneuron = strcmp(Celltype_iHP,'Interneruon') & mask_iHP_HighStability & mask_iHP_HighIsolationQuality;
- mask_iHP_Pyramidal = strcmp(Celltype_iHP,'Pyramidal') & mask_iHP_HighStability & mask_iHP_HighIsolationQuality;
- mask_iHP_NonResponsive=(AvgFr_iHP(:,1) < MeanFR & AvgFr_iHP(:,2) < MeanFR & mask_iHP_HighIsolationQuality & mask_iHP_HighStability & mask_iHP_Pyramidal);
- mask_iHP_Responsive_Both=((AvgFr_iHP(:,1) >= MeanFR & AvgFr_iHP(:,2) >= MeanFR) & mask_iHP_HighIsolationQuality & mask_iHP_HighStability & mask_iHP_Pyramidal);
- mask_iHP_Responsive_OpenField=((AvgFr_iHP(:,1) >= MeanFR) & mask_iHP_HighIsolationQuality & mask_iHP_HighStability & mask_iHP_Pyramidal);
- mask_iHP_Responsive_RadialMaze=((AvgFr_iHP(:,2) >= MeanFR) & mask_iHP_HighIsolationQuality & mask_iHP_HighStability & mask_iHP_Pyramidal);
- LowScoreCLST.iHP=(Assessment_iHP(iHP' & main_iHP_exp & mask_iHP_LowIsolationQuality));
- LowStabilityCLST.iHP=(Assessment_iHP(iHP' & main_iHP_exp & mask_iHP_LowStability));
- AnalyzableCLST.iHP_INT=(Assessment_iHP(iHP' & main_iHP_exp & mask_iHP_Interneuron));
- AnalyzableCLST.iHP_PYR=(Assessment_iHP(iHP' & main_iHP_exp & mask_iHP_Pyramidal));
- AnalyzableCLST.iHP_PYR_NonResp=(Assessment_iHP(iHP' & main_iHP_exp & mask_iHP_NonResponsive));
- AnalyzableCLST.iHP_PYR_Resp_Both=(Assessment_iHP(iHP' & main_iHP_exp & mask_iHP_Responsive_Both));
- AnalyzableCLST.iHP_PYR_Resp_OpenField=(Assessment_iHP(iHP' & main_iHP_exp & mask_iHP_Responsive_OpenField));
- AnalyzableCLST.iHP_PYR_Resp_RadialMaze=(Assessment_iHP(iHP' & main_iHP_exp & mask_iHP_Responsive_RadialMaze));
- %
- AnalyzableCLST.vHP_INT=(Assessment_iHP(vHP' & main_iHP_exp & mask_iHP_Interneuron));
- AnalyzableCLST.vHP_PYR=(Assessment_iHP(vHP' & main_iHP_exp & mask_iHP_Pyramidal));
- AnalyzableCLST.vHP_PYR_NonResp=(Assessment_iHP(vHP' & main_iHP_exp & mask_iHP_NonResponsive));
- AnalyzableCLST.vHP_PYR_Resp_Both=(Assessment_iHP(vHP' & main_iHP_exp & mask_iHP_Responsive_Both));
- AnalyzableCLST.vHP_PYR_Resp_OpenField=(Assessment_iHP(vHP' & main_iHP_exp & mask_iHP_Responsive_OpenField));
- AnalyzableCLST.vHP_PYR_Resp_RadialMaze=(Assessment_iHP(vHP' & main_iHP_exp & mask_iHP_Responsive_RadialMaze));
- % % ****** Calculate the number of cells in Figure 1D ****** % %
- celltype.dHP_Total=length(Assessment_dHP);
- celltype.dHP_Both=length(AnalyzableCLST.dHP_PYR_Resp_Both);
- celltype.dHP_OpenField=length(AnalyzableCLST.dHP_PYR_Resp_OpenField)-celltype.dHP_Both;
- celltype.dHP_RadialMaze=length(AnalyzableCLST.dHP_PYR_Resp_RadialMaze)-celltype.dHP_Both;
- celltype.dHP_NonResp=length(AnalyzableCLST.dHP_PYR_NonResp);
- celltype.iHP_Total=length(iHP' & Assessment_iHP);
- celltype.iHP_Both=length(AnalyzableCLST.iHP_PYR_Resp_Both);
- celltype.iHP_OpenField=length(AnalyzableCLST.iHP_PYR_Resp_OpenField)-celltype.iHP_Both;
- celltype.iHP_RadialMaze=length(AnalyzableCLST.iHP_PYR_Resp_RadialMaze)-celltype.iHP_Both;
- celltype.iHP_NonResp=length(AnalyzableCLST.iHP_PYR_NonResp);
- celltype.vHP_Total=length(vHP' & Assessment_iHP);
- celltype.vHP_Both=length(AnalyzableCLST.vHP_PYR_Resp_Both);
- celltype.vHP_OpenField=length(AnalyzableCLST.vHP_PYR_Resp_OpenField)-celltype.vHP_Both;
- celltype.vHP_RadialMaze=length(AnalyzableCLST.vHP_PYR_Resp_RadialMaze)-celltype.vHP_Both;
- celltype.vHP_NonResp=length(AnalyzableCLST.vHP_PYR_NonResp);
- x=[celltype.dHP_Both celltype.dHP_OpenField celltype.dHP_RadialMaze celltype.dHP_NonResp];
- y=[celltype.iHP_Both celltype.iHP_OpenField celltype.iHP_RadialMaze celltype.iHP_NonResp];
- z=[celltype.vHP_Both celltype.vHP_OpenField celltype.vHP_RadialMaze celltype.vHP_NonResp];
- % % ****** Plotting the pie chart ****** % %
- sum(x)
- fig=figure;
- pie(x)
- sum(y)
- fig=figure;
- pie(y)
- sum(z)
- fig=figure;
- pie(z)
- % % ****** Statistical testing ****** % %
- x=[celltype.dHP_OpenField celltype.dHP_Total-celltype.dHP_OpenField];
- y=[celltype.dHP_RadialMaze celltype.dHP_Total-celltype.dHP_RadialMaze];
- [~,p,stat]=chi2cont([x;y]);
- x=[celltype.iHP_OpenField celltype.iHP_Total-celltype.iHP_OpenField];
- y=[celltype.iHP_RadialMaze celltype.iHP_Total-celltype.iHP_RadialMaze];
- [~,p,stat]=chi2cont([x;y]);
- x=[celltype.vHP_OpenField celltype.vHP_Total-celltype.vHP_OpenField];
- y=[celltype.vHP_RadialMaze celltype.vHP_Total-celltype.vHP_RadialMaze];
- [~,p,stat]=chi2cont([x;y]);
- %% Figure 1E, Mean firing rate
- clear all
- load('Analyzable Unit Information.mat');
- main_dHP_exp = strcmp(SessionType_dHP,'SS') | strcmp(SessionType_dHP,'SSCH1') | strcmp(SessionType_dHP,'SSCH2') | strcmp(SessionType_dHP,'FRCH1') |...
- strcmp(SessionType_dHP,'FRCH2') | strcmp(SessionType_dHP,'SSFR1') | strcmp(SessionType_dHP,'SSFR2') | strcmp(SessionType_dHP,'T-SSCH1') |...
- strcmp(SessionType_dHP,'T-SSCH2') | strcmp(SessionType_dHP,'T-Quantity1') | strcmp(SessionType_dHP,'T-Quantity2');
- main_iHP_exp = strcmp(SessionType_iHP,'SS') | strcmp(SessionType_iHP,'SSCH1') | strcmp(SessionType_iHP,'SSCH2') | strcmp(SessionType_iHP,'FRCH1') |...
- strcmp(SessionType_iHP,'FRCH2') | strcmp(SessionType_iHP,'SSFR1') | strcmp(SessionType_iHP,'SSFR2') | strcmp(SessionType_iHP,'T-SSCH1') |...
- strcmp(SessionType_iHP,'T-SSCH2') | strcmp(SessionType_iHP,'T-Quantity1') | strcmp(SessionType_iHP,'T-Quantity2');
- iHP = DepthFromCortex_iHP < 5.5;
- vHP = DepthFromCortex_iHP >= 5.5;
- mask_dHP_LowIsolationQuality=(Assessment_dHP < 2);
- mask_dHP_HighIsolationQuality = ~mask_dHP_LowIsolationQuality;
- mask_dHP_LowStability=(NumberOfSpike_dHP(:,1)==0 | NumberOfSpike_dHP(:,4)==0) & mask_dHP_HighIsolationQuality;
- mask_dHP_HighStability = ~mask_dHP_LowStability;
- mask_dHP_GoodCluster=mask_dHP_HighStability & mask_dHP_HighIsolationQuality;
- %
- mask_iHP_LowIsolationQuality=(Assessment_iHP < 2);
- mask_iHP_HighIsolationQuality = ~mask_iHP_LowIsolationQuality;
- mask_iHP_LowStability=(NumberOfSpike_iHP(:,1)==0 | NumberOfSpike_iHP(:,4)==0) & mask_iHP_HighIsolationQuality;
- mask_iHP_HighStability = ~mask_iHP_LowStability;
- mask_iHP_GoodCluster=mask_iHP_HighStability & mask_iHP_HighIsolationQuality;
- clear PopulationAvgFr
- a=1; b=1;
- for cl=1:length(Celltype_dHP)
- if isequal(Celltype_dHP{cl},'Pyramidal') && mask_dHP_GoodCluster(cl)==1 && main_dHP_exp(cl)==1
- PopulationAvgFr.Pre_dHP_PYR(a)=PreSleepRate_dHP(cl);
- PopulationAvgFr.Main_dHP_PYR(a)=AvgFr_dHP(cl,2); a=a+1;
- elseif isequal(Celltype_dHP{cl},'Interneruon') && mask_dHP_GoodCluster(cl)==1 && main_dHP_exp(cl)==1
- PopulationAvgFr.Pre_dHP_INT(b)=PreSleepRate_dHP(cl);
- PopulationAvgFr.Main_dHP_INT(b)=AvgFr_dHP(cl,2); b=b+1;
- end
- end
- PopulationAvgFr_Rat.Pre_dHP_PYR{1}=[];
- PopulationAvgFr_Rat.Pre_dHP_PYR{2}=[];
- PopulationAvgFr_Rat.Pre_dHP_PYR{3}=[];
- PopulationAvgFr_Rat.Pre_dHP_PYR{4}=[];
- PopulationAvgFr_Rat.Pre_dHP_PYR{5}=[];
- PopulationAvgFr_Rat.Pre_dHP_PYR{6}=[];
- PopulationAvgFr_Rat.Main_dHP_PYR{1}=[];
- PopulationAvgFr_Rat.Main_dHP_PYR{2}=[];
- PopulationAvgFr_Rat.Main_dHP_PYR{3}=[];
- PopulationAvgFr_Rat.Main_dHP_PYR{4}=[];
- PopulationAvgFr_Rat.Main_dHP_PYR{5}=[];
- PopulationAvgFr_Rat.Main_dHP_PYR{6}=[];
- for cl=1:length(Celltype_dHP)
- [Rat, Type, Day, TetrodeNumber, ClusterNumber, Session, Sessiontype, Index1] = GetSessionInfo(Clstname_dHP{cl});
- Rat=str2num(Rat);
- if isequal(Celltype_dHP{cl},'Pyramidal') && mask_dHP_GoodCluster(cl)==1 && main_dHP_exp(cl)==1
- switch Rat
- case 448
- PopulationAvgFr_Rat.Pre_dHP_PYR{1}(end+1)=PreSleepRate_dHP(cl);
- PopulationAvgFr_Rat.Main_dHP_PYR{1}(end+1)=AvgFr_dHP(cl,2);
- case 459
- PopulationAvgFr_Rat.Pre_dHP_PYR{2}(end+1)=PreSleepRate_dHP(cl);
- PopulationAvgFr_Rat.Main_dHP_PYR{2}(end+1)=AvgFr_dHP(cl,2);
- case 463
- PopulationAvgFr_Rat.Pre_dHP_PYR{3}(end+1)=PreSleepRate_dHP(cl);
- PopulationAvgFr_Rat.Main_dHP_PYR{3}(end+1)=AvgFr_dHP(cl,2);
- case 473
- PopulationAvgFr_Rat.Pre_dHP_PYR{4}(end+1)=PreSleepRate_dHP(cl);
- PopulationAvgFr_Rat.Main_dHP_PYR{4}(end+1)=AvgFr_dHP(cl,2);
- case 488
- PopulationAvgFr_Rat.Pre_dHP_PYR{5}(end+1)=PreSleepRate_dHP(cl);
- PopulationAvgFr_Rat.Main_dHP_PYR{5}(end+1)=AvgFr_dHP(cl,2);
- case 509
- PopulationAvgFr_Rat.Pre_dHP_PYR{6}(end+1)=PreSleepRate_dHP(cl);
- PopulationAvgFr_Rat.Main_dHP_PYR{6}(end+1)=AvgFr_dHP(cl,2);
- end
- end
- end
- % iHP
- a=1; b=1;
- for cl=1:length(Celltype_iHP)
- if iHP(cl) == 1
- if isequal(Celltype_iHP{cl},'Pyramidal') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1
- PopulationAvgFr.Pre_iHP_PYR(a)=PreSleepRate_iHP(cl);
- PopulationAvgFr.Main_iHP_PYR(a)=AvgFr_iHP(cl,2);
- PopulationDepth.iHP_PYR(a)=DepthFromCortex_iHP(cl); a=a+1;
- elseif isequal(Celltype_iHP{cl},'Interneruon') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1
- PopulationAvgFr.Pre_iHP_INT(b)=PreSleepRate_iHP(cl);
- PopulationAvgFr.Main_iHP_INT(b)=AvgFr_iHP(cl,2);
- PopulationDepth.iHP_INT(b)=DepthFromCortex_iHP(cl); b=b+1;
- end
- end
- end
- PopulationAvgFr_Rat.Pre_iHP_PYR{1}=[];
- PopulationAvgFr_Rat.Pre_iHP_PYR{2}=[];
- PopulationAvgFr_Rat.Pre_iHP_PYR{3}=[];
- PopulationAvgFr_Rat.Pre_iHP_PYR{4}=[];
- PopulationAvgFr_Rat.Pre_iHP_PYR{5}=[];
- PopulationAvgFr_Rat.Pre_iHP_PYR{6}=[];
- PopulationAvgFr_Rat.Main_iHP_PYR{1}=[];
- PopulationAvgFr_Rat.Main_iHP_PYR{2}=[];
- PopulationAvgFr_Rat.Main_iHP_PYR{3}=[];
- PopulationAvgFr_Rat.Main_iHP_PYR{4}=[];
- PopulationAvgFr_Rat.Main_iHP_PYR{5}=[];
- PopulationAvgFr_Rat.Main_iHP_PYR{6}=[];
- for cl=1:length(Celltype_iHP)
- [Rat, Type, Day, TetrodeNumber, ClusterNumber, Session, Sessiontype, Index1] = GetSessionInfo(Clstname_iHP{cl});
- Rat=str2num(Rat);
- if isequal(Celltype_iHP{cl},'Pyramidal') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1 && iHP(cl) == 1
- switch Rat
- case 448
- PopulationAvgFr_Rat.Pre_iHP_PYR{1}(end+1)=PreSleepRate_iHP(cl);
- PopulationAvgFr_Rat.Main_iHP_PYR{1}(end+1)=AvgFr_iHP(cl,2);
- case 459
- PopulationAvgFr_Rat.Pre_iHP_PYR{2}(end+1)=PreSleepRate_iHP(cl);
- PopulationAvgFr_Rat.Main_iHP_PYR{2}(end+1)=AvgFr_iHP(cl,2);
- case 463
- PopulationAvgFr_Rat.Pre_iHP_PYR{3}(end+1)=PreSleepRate_iHP(cl);
- PopulationAvgFr_Rat.Main_iHP_PYR{3}(end+1)=AvgFr_iHP(cl,2);
- case 473
- PopulationAvgFr_Rat.Pre_iHP_PYR{4}(end+1)=PreSleepRate_iHP(cl);
- PopulationAvgFr_Rat.Main_iHP_PYR{4}(end+1)=AvgFr_iHP(cl,2);
- case 488
- PopulationAvgFr_Rat.Pre_iHP_PYR{5}(end+1)=PreSleepRate_iHP(cl);
- PopulationAvgFr_Rat.Main_iHP_PYR{5}(end+1)=AvgFr_iHP(cl,2);
- case 509
- PopulationAvgFr_Rat.Pre_iHP_PYR{6}(end+1)=PreSleepRate_iHP(cl);
- PopulationAvgFr_Rat.Main_iHP_PYR{6}(end+1)=AvgFr_iHP(cl,2);
- end
- end
- end
- % vHP
- a=1; b=1;
- for cl=1:length(Celltype_iHP)
- if vHP(cl) == 1
- if isequal(Celltype_iHP{cl},'Pyramidal') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1
- PopulationAvgFr.Pre_vHP_PYR(a)=PreSleepRate_iHP(cl);
- PopulationAvgFr.Main_vHP_PYR(a)=AvgFr_iHP(cl,2);a=a+1;
- elseif isequal(Celltype_iHP{cl},'Interneruon') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1
- PopulationAvgFr.Pre_iHP_INT(b)=PreSleepRate_iHP(cl);
- PopulationAvgFr.Main_vHP_INT(b)=AvgFr_iHP(cl,2);b=b+1;
- end
- end
- end
- PopulationAvgFr_Rat.Pre_vHP_PYR{1}=[];
- PopulationAvgFr_Rat.Pre_vHP_PYR{2}=[];
- PopulationAvgFr_Rat.Pre_vHP_PYR{3}=[];
- PopulationAvgFr_Rat.Pre_vHP_PYR{4}=[];
- PopulationAvgFr_Rat.Pre_vHP_PYR{5}=[];
- PopulationAvgFr_Rat.Pre_vHP_PYR{6}=[];
- PopulationAvgFr_Rat.Main_vHP_PYR{1}=[];
- PopulationAvgFr_Rat.Main_vHP_PYR{2}=[];
- PopulationAvgFr_Rat.Main_vHP_PYR{3}=[];
- PopulationAvgFr_Rat.Main_vHP_PYR{4}=[];
- PopulationAvgFr_Rat.Main_vHP_PYR{5}=[];
- PopulationAvgFr_Rat.Main_vHP_PYR{6}=[];
- for cl=1:length(Celltype_iHP)
- [Rat, Type, Day, TetrodeNumber, ClusterNumber, Session, Sessiontype, Index1] = GetSessionInfo(Clstname_iHP{cl});
- Rat=str2num(Rat);
- if isequal(Celltype_iHP{cl},'Pyramidal') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1 && vHP(cl) == 1
- switch Rat
- case 448
- PopulationAvgFr_Rat.Pre_vHP_PYR{1}(end+1)=PreSleepRate_iHP(cl);
- PopulationAvgFr_Rat.Main_vHP_PYR{1}(end+1)=AvgFr_iHP(cl,2);
- case 459
- PopulationAvgFr_Rat.Pre_vHP_PYR{2}(end+1)=PreSleepRate_iHP(cl);
- PopulationAvgFr_Rat.Main_vHP_PYR{2}(end+1)=AvgFr_iHP(cl,2);
- case 463
- PopulationAvgFr_Rat.Pre_vHP_PYR{3}(end+1)=PreSleepRate_iHP(cl);
- PopulationAvgFr_Rat.Main_vHP_PYR{3}(end+1)=AvgFr_iHP(cl,2);
- case 473
- PopulationAvgFr_Rat.Pre_vHP_PYR{4}(end+1)=PreSleepRate_iHP(cl);
- PopulationAvgFr_Rat.Main_vHP_PYR{4}(end+1)=AvgFr_iHP(cl,2);
- case 488
- PopulationAvgFr_Rat.Pre_vHP_PYR{5}(end+1)=PreSleepRate_iHP(cl);
- PopulationAvgFr_Rat.Main_vHP_PYR{5}(end+1)=AvgFr_iHP(cl,2);
- case 509
- PopulationAvgFr_Rat.Pre_vHP_PYR{6}(end+1)=PreSleepRate_iHP(cl);
- PopulationAvgFr_Rat.Main_vHP_PYR{6}(end+1)=AvgFr_iHP(cl,2);
- end
- end
- end
- % % ****** Plotting the mean +/- s.t.d grpah****** % %
- fig=figure; hold on;
- fig.Position=[0 0 1000 500];
- Color.color=2; Color.alpha=1;
- Jin_MeanSTE_Line(1,PopulationAvgFr.Pre_dHP_PYR,Color);
- for i=1:6
- plot(1, mean(PopulationAvgFr_Rat.Pre_dHP_PYR{i}),'r.')
- end
- Color.color=1;
- Jin_MeanSTE_Line(1,PopulationAvgFr.Pre_iHP_PYR,Color)
- for i=1:6
- plot(1, mean(PopulationAvgFr_Rat.Pre_iHP_PYR{i}),'b.')
- end
- Color.color=3;
- Jin_MeanSTE_Line(1,PopulationAvgFr.Pre_vHP_PYR,Color)
- for i=1:6
- plot(1, mean(PopulationAvgFr_Rat.Pre_vHP_PYR{i}),'g.')
- end
- Color.color=2; Color.alpha=1;
- Jin_MeanSTE_Line(2,PopulationAvgFr.Main_dHP_PYR,Color)
- for i=1:6
- plot(2, mean(PopulationAvgFr_Rat.Main_dHP_PYR{i}),'r.')
- end
- Color.color=1;
- Jin_MeanSTE_Line(2,PopulationAvgFr.Main_iHP_PYR,Color)
- for i=1:6
- plot(2, mean(PopulationAvgFr_Rat.Main_iHP_PYR{i}),'b.')
- end
- Color.color=3;
- Jin_MeanSTE_Line(2,PopulationAvgFr.Main_vHP_PYR,Color)
- for i=1:6
- plot(2, mean(PopulationAvgFr_Rat.Main_vHP_PYR{i}),'g.')
- end
- g=gca; g.YLim=[0.4 2]; g.YTick=0:0.4:2;
- % % Statistical testing
- % % Two way mixed ANOVA
- dHP_Pre=[PopulationAvgFr.Pre_dHP_PYR]';
- dHP_Main=[PopulationAvgFr.Main_dHP_PYR]';
- iHP_Pre=[PopulationAvgFr.Pre_iHP_PYR]';
- iHP_Main=[PopulationAvgFr.Main_iHP_PYR]';
- vHP_Pre=[PopulationAvgFr.Pre_vHP_PYR]';
- vHP_Main=[PopulationAvgFr.Main_vHP_PYR]';
- Y = [dHP_Pre; dHP_Main; iHP_Pre; iHP_Main; vHP_Pre; vHP_Main];
- BS = [GetGroupingVar(dHP_Pre,1); GetGroupingVar(dHP_Main,1); GetGroupingVar(iHP_Pre,2); GetGroupingVar(iHP_Main,2); GetGroupingVar(vHP_Pre,3); GetGroupingVar(vHP_Main,3)];
- WS = [GetGroupingVar(dHP_Pre,1); GetGroupingVar(dHP_Main,2); GetGroupingVar(iHP_Pre,1); GetGroupingVar(iHP_Main,2); GetGroupingVar(vHP_Pre,1); GetGroupingVar(vHP_Main,2)];
- S = [GetGroupingVar(dHP_Pre); GetGroupingVar(dHP_Main); GetGroupingVar(iHP_Pre)+length(dHP_Pre); GetGroupingVar(iHP_Main)+length(dHP_Pre); GetGroupingVar(vHP_Pre)+length(dHP_Pre)+length(iHP_Pre); GetGroupingVar(vHP_Main)+length(dHP_Pre)+length(iHP_Pre)];
- X = [Y BS WS S];
- [SSQs, DFs, MSQs, Fs, Ps] = Stat_ANOVA2_Mixed(X);
- [h,p,~,stat]=ttest2(iHP_Pre, vHP_Pre)
- [h,p,~,stat]=ttest2(iHP_Main, vHP_Main)
- %% Figure 1F, Theta-modulation index
- clear all
- load('Analyzable Unit Information.mat');
- main_dHP_exp = strcmp(SessionType_dHP,'SS') | strcmp(SessionType_dHP,'SSCH1') | strcmp(SessionType_dHP,'SSCH2') | strcmp(SessionType_dHP,'FRCH1') |...
- strcmp(SessionType_dHP,'FRCH2') | strcmp(SessionType_dHP,'SSFR1') | strcmp(SessionType_dHP,'SSFR2') | strcmp(SessionType_dHP,'T-SSCH1') |...
- strcmp(SessionType_dHP,'T-SSCH2') | strcmp(SessionType_dHP,'T-Quantity1') | strcmp(SessionType_dHP,'T-Quantity2');
- main_iHP_exp = strcmp(SessionType_iHP,'SS') | strcmp(SessionType_iHP,'SSCH1') | strcmp(SessionType_iHP,'SSCH2') | strcmp(SessionType_iHP,'FRCH1') |...
- strcmp(SessionType_iHP,'FRCH2') | strcmp(SessionType_iHP,'SSFR1') | strcmp(SessionType_iHP,'SSFR2') | strcmp(SessionType_iHP,'T-SSCH1') |...
- strcmp(SessionType_iHP,'T-SSCH2') | strcmp(SessionType_iHP,'T-Quantity1') | strcmp(SessionType_iHP,'T-Quantity2');
- iHP = DepthFromCortex_iHP < 5.5;
- vHP = DepthFromCortex_iHP >= 5.5;
- mask_dHP_LowIsolationQuality=(Assessment_dHP < 2);
- mask_dHP_HighIsolationQuality = ~mask_dHP_LowIsolationQuality;
- mask_dHP_LowStability=(NumberOfSpike_dHP(:,1)==0 | NumberOfSpike_dHP(:,4)==0) & mask_dHP_HighIsolationQuality;
- mask_dHP_HighStability = ~mask_dHP_LowStability;
- mask_dHP_GoodCluster=mask_dHP_HighStability & mask_dHP_HighIsolationQuality;
- %
- mask_iHP_LowIsolationQuality=(Assessment_iHP < 2);
- mask_iHP_HighIsolationQuality = ~mask_iHP_LowIsolationQuality;
- mask_iHP_LowStability=(NumberOfSpike_iHP(:,1)==0 | NumberOfSpike_iHP(:,4)==0) & mask_iHP_HighIsolationQuality;
- mask_iHP_HighStability = ~mask_iHP_LowStability;
- mask_iHP_GoodCluster=mask_iHP_HighStability & mask_iHP_HighIsolationQuality;
- a=1; b=1;
- for cl=1:length(Celltype_dHP)
- if sum(Populationcorrelogram.dHP(cl,:)) > 100 && main_dHP_exp(cl)==1
- if isequal(Celltype_dHP{cl},'Pyramidal')
- PopulationCorrelogram.dHP_PYR(a,:)=PopulationCorrelogram.dHP(cl,:)./max(PopulationCorrelogram.dHP(cl,62:65));
- PopulationTMI.dHP_PYR(a)=PopulationTMI.dHP(cl);
- a=a+1;
- elseif isequal(Celltype_dHP{cl},'Interneruon')
- PopulationCorrelogram.dHP_INT(b,:)=PopulationCorrelogram.dHP(cl,:)./max(PopulationCorrelogram.dHP(cl,62:65));
- PopulationTMI.dHP_INT(b)=PopulationTMI.dHP(cl);
- b=b+1;
- end
- end
- end
-
- a=1; b=1;
- for cl=1:length(Celltype_iHP)
- if sum(Populationcorrelogram.iHP(cl,:)) > 100 && DepthFromCortex_iHP(cl) < 5.5 && main_iHP_exp(cl)==1
- if isequal(Celltype_iHP{cl},'Pyramidal')
- PopulationCorrelogram.iHP_PYR(a,:)=PopulationCorrelogram.iHP(cl,:)./max(PopulationCorrelogram.iHP(cl,62:65));
- PopulationTMI.iHP_PYR(a)=PopulationTMI.iHP(cl);
- PopulationDepthIndex.iHP_PYR(a)=PopulationDepthIndex.iHP(cl);
- a=a+1;
- elseif isequal(Celltype_iHP{cl},'Interneruon')
- PopulationCorrelogram.iHP_INT(b,:)=PopulationCorrelogram.iHP(cl,:)./max(PopulationCorrelogram.iHP(cl,62:65));
- PopulationTMI.iHP_INT(b)=PopulationTMI.iHP(cl);
- PopulationDepthIndex.iHP_INT(b)=PopulationDepthIndex.iHP(cl);
- b=b+1;
- end
- end
- end
- a=1; b=1;
- for cl=1:length(Celltype_iHP)
- if sum(Populationcorrelogram.iHP(cl,:)) > 100 && DepthFromCortex_iHP(cl) >= 5.5 && main_iHP_exp(cl)==1
- if isequal(Celltype_iHP{cl},'Pyramidal')
- PopulationCorrelogram.vHP_PYR(a,:)=PopulationCorrelogram.iHP(cl,:)./max(PopulationCorrelogram.iHP(cl,62:65));
- PopulationTMI.vHP_PYR(a)=PopulationTMI.iHP(cl);
- PopulationDepthIndex.vHP_PYR(a)=PopulationDepthIndex.iHP(cl);
- a=a+1;
- elseif isequal(Celltype_iHP{cl},'Interneruon')
- PopulationCorrelogram.vHP_INT(b,:)=PopulationCorrelogram.iHP(cl,:)./max(PopulationCorrelogram.iHP(cl,62:65));
- PopulationTMI.vHP_INT(b)=PopulationTMI.iHP(cl);
- PopulationDepthIndex.vHP_INT(b)=PopulationDepthIndex.iHP(cl);
- b=b+1;
- end
- end
- end
- PopulationBasicFr_Rat.TMI_dHP_PYR{1}=[];
- PopulationBasicFr_Rat.TMI_dHP_PYR{2}=[];
- PopulationBasicFr_Rat.TMI_dHP_PYR{3}=[];
- PopulationBasicFr_Rat.TMI_dHP_PYR{4}=[];
- PopulationBasicFr_Rat.TMI_dHP_PYR{5}=[];
- PopulationBasicFr_Rat.TMI_dHP_PYR{6}=[];
- for cl=1:length(Celltype_dHP)
- [Rat, Type, Day, TetrodeNumber, ClusterNumber, Session, Sessiontype, Index1] = GetSessionInfo(Clstname_dHP{cl});
- Rat=str2num(Rat);
- if isequal(Celltype_dHP{cl},'Pyramidal') && mask_dHP_GoodCluster(cl)==1 && main_dHP_exp(cl)==1 && sum(Populationcorrelogram.dHP(cl,:)) > 100
- switch Rat
- case 448
- PopulationBasicFr_Rat.TMI_dHP_PYR{1}(end+1)=PopulationTMI.dHP(cl);
- case 459
- PopulationBasicFr_Rat.TMI_dHP_PYR{2}(end+1)=PopulationTMI.dHP(cl);
- case 463
- PopulationBasicFr_Rat.TMI_dHP_PYR{3}(end+1)=PopulationTMI.dHP(cl);
- case 473
- PopulationBasicFr_Rat.TMI_dHP_PYR{4}(end+1)=PopulationTMI.dHP(cl);
- case 488
- % PopulationBasicFr_Rat.TMI_dHP_PYR{5}(end+1)=TMI_dHP(cl);
- case 509
- PopulationBasicFr_Rat.TMI_dHP_PYR{6}(end+1)=PopulationTMI.dHP(cl);
- end
- end
- end
- PopulationBasicFr_Rat.TMI_iHP_PYR{1}=[];
- PopulationBasicFr_Rat.TMI_iHP_PYR{2}=[];
- PopulationBasicFr_Rat.TMI_iHP_PYR{3}=[];
- PopulationBasicFr_Rat.TMI_iHP_PYR{4}=[];
- PopulationBasicFr_Rat.TMI_iHP_PYR{5}=[];
- PopulationBasicFr_Rat.TMI_iHP_PYR{6}=[];
- for cl=1:length(Celltype_iHP)
- [Rat, Type, Day, TetrodeNumber, ClusterNumber, Session, Sessiontype, Index1] = GetSessionInfo(Clstname_iHP{cl});
- Rat=str2num(Rat);
- if isequal(Celltype_iHP{cl},'Pyramidal') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1 && sum(Populationcorrelogram.iHP(cl,:)) > 100 && iHP(cl) == 1
- switch Rat
- case 448
- PopulationBasicFr_Rat.TMI_iHP_PYR{1}(end+1)=PopulationTMI.iHP(cl);
- case 459
- PopulationBasicFr_Rat.TMI_iHP_PYR{2}(end+1)=PopulationTMI.iHP(cl);
- case 463
- PopulationBasicFr_Rat.TMI_iHP_PYR{3}(end+1)=PopulationTMI.iHP(cl);
- case 473
- PopulationBasicFr_Rat.TMI_iHP_PYR{4}(end+1)=PopulationTMI.iHP(cl);
- case 488
- % PopulationBasicFr_Rat.TMI_iHP_PYR{5}(end+1)=PopulationTMI.iHP(cl);
- case 509
- PopulationBasicFr_Rat.TMI_iHP_PYR{6}(end+1)=PopulationTMI.iHP(cl);
- end
- end
- end
- PopulationBasicFr_Rat.TMI_vHP_PYR{1}=[];
- PopulationBasicFr_Rat.TMI_vHP_PYR{2}=[];
- PopulationBasicFr_Rat.TMI_vHP_PYR{3}=[];
- PopulationBasicFr_Rat.TMI_vHP_PYR{4}=[];
- PopulationBasicFr_Rat.TMI_vHP_PYR{5}=[];
- PopulationBasicFr_Rat.TMI_vHP_PYR{6}=[];
- for cl=1:length(Celltype_iHP)
- [Rat, Type, Day, TetrodeNumber, ClusterNumber, Session, Sessiontype, Index1] = GetSessionInfo(Clstname_iHP{cl});
- Rat=str2num(Rat);
- if isequal(Celltype_iHP{cl},'Pyramidal') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1 && sum(Populationcorrelogram.iHP(cl,:)) > 100 && vHP(cl) == 1
- switch Rat
- case 448
- PopulationBasicFr_Rat.TMI_vHP_PYR{1}(end+1)=PopulationTMI.iHP(cl);
- case 459
- PopulationBasicFr_Rat.TMI_vHP_PYR{2}(end+1)=PopulationTMI.iHP(cl);
- case 463
- PopulationBasicFr_Rat.TMI_vHP_PYR{3}(end+1)=PopulationTMI.iHP(cl);
- case 473
- PopulationBasicFr_Rat.TMI_vHP_PYR{4}(end+1)=PopulationTMI.iHP(cl);
- case 488
- PopulationBasicFr_Rat.TMI_vHP_PYR{5}(end+1)=PopulationTMI.iHP(cl);
- case 509
- PopulationBasicFr_Rat.TMI_vHP_PYR{6}(end+1)=PopulationTMI.iHP(cl);
- end
- end
- end
- % % Plotting
- fig=figure; hold on;
- fig.Position=[0 0 1000 500];
- Color.color=2; Color.alpha=1;
- Jin_MeanSTE_Line(1,PopulationTMI.dHP_PYR,Color)
- for i=1:6
- plot(1, mean(PopulationBasicFr_Rat.TMI_dHP_PYR{i}),'r.')
- end
- Color.color=1;
- Jin_MeanSTE_Line(2,PopulationTMI.iHP_PYR,Color)
- for i=1:6
- plot(2, mean(PopulationBasicFr_Rat.TMI_iHP_PYR{i}),'b.')
- end
- Color.color=3;
- Jin_MeanSTE_Line(3,PopulationTMI.vHP_PYR,Color)
- for i=1:6
- plot(3, mean(PopulationBasicFr_Rat.TMI_vHP_PYR{i}),'g.')
- end
- % % Statistical testing
- dHP_PYR=[PopulationTMI.dHP_PYR]';
- iHP_PYR=[PopulationTMI.iHP_PYR]';
- vHP_PYR=[PopulationTMI.vHP_PYR]';
- % %
- Y = [dHP_PYR; iHP_PYR; vHP_PYR];
- GROUP = [GetGroupingVar(dHP_PYR,1); GetGroupingVar(iHP_PYR,12); GetGroupingVar(vHP_PYR,3)];
- [Pvalue, result, gnames] = Stat_ANOVA1(Y,GROUP);
- %% Figure 1G, Bursting index
- clear all
- load('Analyzable Unit Information.mat');
- main_dHP_exp = strcmp(SessionType_dHP,'SS') | strcmp(SessionType_dHP,'SSCH1') | strcmp(SessionType_dHP,'SSCH2') | strcmp(SessionType_dHP,'FRCH1') |...
- strcmp(SessionType_dHP,'FRCH2') | strcmp(SessionType_dHP,'SSFR1') | strcmp(SessionType_dHP,'SSFR2') | strcmp(SessionType_dHP,'T-SSCH1') |...
- strcmp(SessionType_dHP,'T-SSCH2') | strcmp(SessionType_dHP,'T-Quantity1') | strcmp(SessionType_dHP,'T-Quantity2');
- main_iHP_exp = strcmp(SessionType_iHP,'SS') | strcmp(SessionType_iHP,'SSCH1') | strcmp(SessionType_iHP,'SSCH2') | strcmp(SessionType_iHP,'FRCH1') |...
- strcmp(SessionType_iHP,'FRCH2') | strcmp(SessionType_iHP,'SSFR1') | strcmp(SessionType_iHP,'SSFR2') | strcmp(SessionType_iHP,'T-SSCH1') |...
- strcmp(SessionType_iHP,'T-SSCH2') | strcmp(SessionType_iHP,'T-Quantity1') | strcmp(SessionType_iHP,'T-Quantity2');
- iHP = DepthFromCortex_iHP < 5.5;
- vHP = DepthFromCortex_iHP >= 5.5;
- mask_dHP_LowIsolationQuality=(Assessment_dHP < 2);
- mask_dHP_HighIsolationQuality = ~mask_dHP_LowIsolationQuality;
- mask_dHP_LowStability=(NumberOfSpike_dHP(:,1)==0 | NumberOfSpike_dHP(:,4)==0) & mask_dHP_HighIsolationQuality;
- mask_dHP_HighStability = ~mask_dHP_LowStability;
- mask_dHP_GoodCluster=mask_dHP_HighStability & mask_dHP_HighIsolationQuality;
- %
- mask_iHP_LowIsolationQuality=(Assessment_iHP < 2);
- mask_iHP_HighIsolationQuality = ~mask_iHP_LowIsolationQuality;
- mask_iHP_LowStability=(NumberOfSpike_iHP(:,1)==0 | NumberOfSpike_iHP(:,4)==0) & mask_iHP_HighIsolationQuality;
- mask_iHP_HighStability = ~mask_iHP_LowStability;
- mask_iHP_GoodCluster=mask_iHP_HighStability & mask_iHP_HighIsolationQuality;
- a=1; b=1;
- for cl=1:length(Celltype_dHP)
- if sum(Populationcorrelogram.dHP(cl,:)) > 100
- if isequal(Celltype_dHP{cl},'Pyramidal') && mask_dHP_GoodCluster(cl)==1 && main_dHP_exp(cl)==1
- PopulationBasicFr.BurstingIndex_dHP_PYR(a)=BurstingIndex_dHP(cl,2);
- PopulationBasicFr.SpikeWidth_dHP_PYR(a)=SpikeWidth_dHP(cl); a=a+1;
- elseif isequal(Celltype_dHP{cl},'Interneruon') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1
- PopulationBasicFr.BurstingIndex_dHP_INT(b)=BurstingIndex_dHP(cl,2);
- PopulationBasicFr.SpikeWidth_dHP_INT(b)=SpikeWidth_dHP(cl); b=b+1;
- end
- end
- end
-
- a=1; b=1;
- for cl=1:length(Celltype_iHP)
- if sum(Populationcorrelogram.iHP(cl,:)) > 100
- if isequal(Celltype_iHP{cl},'Pyramidal') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1 && iHP(cl) == 1
- PopulationBasicFr.BurstingIndex_iHP_PYR(a)=BurstingIndex_iHP(cl,2);
- PopulationBasicFr.SpikeWidth_iHP_PYR(a)=SpikeWidth_iHP(cl);
- PopulationDepth.iHP_PYR(a)=DepthFromCortex_iHP(cl); a=a+1;
- elseif isequal(Celltype_iHP{cl},'Interneruon') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1 && iHP(cl) == 1
- PopulationBasicFr.BurstingIndex_iHP_INT(b)=BurstingIndex_iHP(cl,2);
- PopulationBasicFr.SpikeWidth_iHP_INT(b)=SpikeWidth_iHP(cl);
- PopulationDepth.iHP_INT(b)=DepthFromCortex_iHP(cl); b=b+1;
- end
- end
- end
-
- a=1; b=1;
- for cl=1:length(Celltype_iHP)
- if sum(Populationcorrelogram.iHP(cl,:)) > 100
- if isequal(Celltype_iHP{cl},'Pyramidal') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1 && vHP(cl) == 1
- PopulationBasicFr.BurstingIndex_vHP_PYR(a)=BurstingIndex_iHP(cl,2);
- PopulationBasicFr.SpikeWidth_vHP_PYR(a)=SpikeWidth_iHP(cl);
- PopulationDepth.vHP_PYR(a)=DepthFromCortex_iHP(cl); a=a+1;
- elseif isequal(Celltype_iHP{cl},'Interneruon') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1 && vHP(cl) == 1
- PopulationBasicFr.BurstingIndex_vHP_INT(b)=BurstingIndex_iHP(cl,2);
- PopulationBasicFr.SpikeWidth_vHP_INT(b)=SpikeWidth_iHP(cl);
- PopulationDepth.vHP_INT(b)=DepthFromCortex_iHP(cl); b=b+1;
- end
- end
- end
- PopulationBasicFr_Rat.BurstingIndex_dHP_PYR{1}=[];
- PopulationBasicFr_Rat.BurstingIndex_dHP_PYR{2}=[];
- PopulationBasicFr_Rat.BurstingIndex_dHP_PYR{3}=[];
- PopulationBasicFr_Rat.BurstingIndex_dHP_PYR{4}=[];
- PopulationBasicFr_Rat.BurstingIndex_dHP_PYR{5}=[];
- PopulationBasicFr_Rat.BurstingIndex_dHP_PYR{6}=[];
- for cl=1:length(Celltype_dHP)
- [Rat, Type, Day, TetrodeNumber, ClusterNumber, Session, Sessiontype, Index1] = GetSessionInfo(Clstname_dHP{cl});
- Rat=str2num(Rat);
- if isequal(Celltype_dHP{cl},'Pyramidal') && mask_dHP_GoodCluster(cl)==1 && main_dHP_exp(cl)==1 && sum(Populationcorrelogram.dHP(cl,:)) > 100
- switch Rat
- case 448
- PopulationBasicFr_Rat.BurstingIndex_dHP_PYR{1}(end+1)=BurstingIndex_dHP(cl,2);
- case 459
- PopulationBasicFr_Rat.BurstingIndex_dHP_PYR{2}(end+1)=BurstingIndex_dHP(cl,2);
- case 463
- PopulationBasicFr_Rat.BurstingIndex_dHP_PYR{3}(end+1)=BurstingIndex_dHP(cl,2);
- case 473
- PopulationBasicFr_Rat.BurstingIndex_dHP_PYR{4}(end+1)=BurstingIndex_dHP(cl,2);
- case 488
- % PopulationBasicFr_Rat.BurstingIndex_dHP_PYR{5}(end+1)=BurstingIndex_dHP(cl,2);
- case 509
- PopulationBasicFr_Rat.BurstingIndex_dHP_PYR{6}(end+1)=BurstingIndex_dHP(cl,2);
- end
- end
- end
- PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{1}=[];
- PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{2}=[];
- PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{3}=[];
- PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{4}=[];
- PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{5}=[];
- PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{6}=[];
- for cl=1:length(Celltype_iHP)
- [Rat, Type, Day, TetrodeNumber, ClusterNumber, Session, Sessiontype, Index1] = GetSessionInfo(Clstname_iHP{cl});
- Rat=str2num(Rat);
- if isequal(Celltype_iHP{cl},'Pyramidal') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1 && sum(Populationcorrelogram.iHP(cl,:)) > 100 && iHP(cl) == 1
- switch Rat
- case 448
- PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{1}(end+1)=BurstingIndex_iHP(cl,2);
- case 459
- PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{2}(end+1)=BurstingIndex_iHP(cl,2);
- case 463
- PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{3}(end+1)=BurstingIndex_iHP(cl,2);
- case 473
- PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{4}(end+1)=BurstingIndex_iHP(cl,2);
- case 488
- % PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{5}(end+1)=BurstingIndex_iHP(cl,2);
- case 509
- PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{6}(end+1)=BurstingIndex_iHP(cl,2);
- end
- end
- end
- PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{1}=[];
- PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{2}=[];
- PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{3}=[];
- PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{4}=[];
- PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{5}=[];
- PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{6}=[];
- for cl=1:length(Celltype_iHP)
- [Rat, Type, Day, TetrodeNumber, ClusterNumber, Session, Sessiontype, Index1] = GetSessionInfo(Clstname_iHP{cl});
- Rat=str2num(Rat);
- if isequal(Celltype_iHP{cl},'Pyramidal') && mask_iHP_GoodCluster(cl)==1 && main_iHP_exp(cl)==1 && sum(Populationcorrelogram.iHP(cl,:)) > 100 && vHP(cl) == 1
- switch Rat
- case 448
- PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{1}(end+1)=BurstingIndex_iHP(cl,2);
- case 459
- PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{2}(end+1)=BurstingIndex_iHP(cl,2);
- case 463
- PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{3}(end+1)=BurstingIndex_iHP(cl,2);
- case 473
- PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{4}(end+1)=BurstingIndex_iHP(cl,2);
- case 488
- PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{5}(end+1)=BurstingIndex_iHP(cl,2);
- case 509
- PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{6}(end+1)=BurstingIndex_iHP(cl,2);
- end
- end
- end
- fig=figure; hold on;
- fig.Position=[0 0 1000 500];
- Color.color=2; Color.alpha=1;
- Jin_MeanSTE_Line(1,PopulationBasicFr.BurstingIndex_dHP_PYR,Color)
- for i=1:6
- plot(1, mean(PopulationBasicFr_Rat.BurstingIndex_dHP_PYR{i}),'r.')
- end
- Color.color=1;
- Jin_MeanSTE_Line(2,PopulationBasicFr.BurstingIndex_iHP_PYR,Color)
- for i=1:6
- % mean(PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{i})
- plot(2, mean(PopulationBasicFr_Rat.BurstingIndex_iHP_PYR{i}),'b.')
- end
- Color.color=3;
- Jin_MeanSTE_Line(3,PopulationBasicFr.BurstingIndex_vHP_PYR,Color)
- for i=1:6
- % mean(PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{i})
- plot(3, mean(PopulationBasicFr_Rat.BurstingIndex_vHP_PYR{i}),'g.')
- end
- % % Statistical testing
- dHP_PYR=[PopulationBasicFr.BurstingIndex_dHP_PYR]';
- iHP_PYR=[PopulationBasicFr.BurstingIndex_iHP_PYR]';
- vHP_PYR=[PopulationBasicFr.BurstingIndex_vHP_PYR]';
- Y = [dHP_PYR; iHP_PYR; vHP_PYR];
- GROUP = [GetGroupingVar(dHP_PYR,1); GetGroupingVar(iHP_PYR,12); GetGroupingVar(vHP_PYR,3)];
- [Pvalue, result, ~] = Stat_ANOVA1(Y,GROUP);
- %% Figure 1H, Spatial information
- clear all
- FR_Thre=0.25;
- pvalue=0.01;
- Color=mapcolor(100,0);
- REGION='Total';
- SI_dHP_Thre=0.25;
- SI_iHP_Thre=0.25;
- load('ClusterInfo_Openfield_Total.mat')
- Active_dHP=ClusterInfo.Total_dHP_AvgFiringRate >= FR_Thre;
- Active_iHP=ClusterInfo.Total_iHP_AvgFiringRate >= FR_Thre;
- Information_dHP = ClusterInfo.Total_dHP_SpatialInfo >= SI_dHP_Thre;
- Information_iHP = ClusterInfo.Total_iHP_SpatialInfo >= SI_iHP_Thre;
- SpatiallyModulated_dHP = ClusterInfo.Total_dHP_SpatialInfo_pvalue < pvalue;
- SpatiallyModulated_iHP = ClusterInfo.Total_iHP_SpatialInfo_pvalue < pvalue;
- PlaceCell_dHP=Active_dHP&Information_dHP&SpatiallyModulated_dHP;
- PlaceCell_iHP=Active_iHP&Information_iHP&SpatiallyModulated_iHP;
- iHP = (ClusterInfo.Total_iHP_DistFromCortex < 5.5);
- vHP = (ClusterInfo.Total_iHP_DistFromCortex >= 5.5);
- % Flag, Rat
- r448_dHP = logical(zeros(1,length(ClusterInfo.Total_dHP_Name)));
- r448_iHP = logical(zeros(1,length(ClusterInfo.Total_iHP_Name)));
- r459_dHP = logical(zeros(1,length(ClusterInfo.Total_dHP_Name)));
- r459_iHP = logical(zeros(1,length(ClusterInfo.Total_iHP_Name)));
- r463_dHP = logical(zeros(1,length(ClusterInfo.Total_dHP_Name)));
- r463_iHP = logical(zeros(1,length(ClusterInfo.Total_iHP_Name)));
- r473_dHP = logical(zeros(1,length(ClusterInfo.Total_dHP_Name)));
- r473_iHP = logical(zeros(1,length(ClusterInfo.Total_iHP_Name)));
- r488_dHP = logical(zeros(1,length(ClusterInfo.Total_dHP_Name)));
- r488_iHP = logical(zeros(1,length(ClusterInfo.Total_iHP_Name)));
- r509_dHP = logical(zeros(1,length(ClusterInfo.Total_dHP_Name)));
- r509_iHP = logical(zeros(1,length(ClusterInfo.Total_iHP_Name)));
- for i=1:1
- for j=1:length(ClusterInfo.Total_iHP_Name)
- name = ClusterInfo.Total_iHP_Name{1,j};
- if ~isempty(name)
- if isequal(name(13:15),'448')
- r448_iHP(i,j) = logical(1);
- end
- if isequal(name(13:15),'459')
- r459_iHP(i,j) = logical(1);
- end
- if isequal(name(13:15),'463')
- r463_iHP(i,j) = logical(1);
- end
- if isequal(name(13:15),'473')
- r473_iHP(i,j) = logical(1);
- end
- if isequal(name(13:15),'488')
- r488_iHP(i,j) = logical(1);
- end
- if isequal(name(13:15),'509')
- r509_iHP(i,j) = logical(1);
- end
- end
- end
- end
- for i=1:1
- for j=1:length(ClusterInfo.Total_dHP_Name)
- name = ClusterInfo.Total_dHP_Name{1,j};
- if ~isempty(name)
- if isequal(name(13:15),'448')
- r448_dHP(i,j) = logical(1);
- end
- if isequal(name(13:15),'459')
- r459_dHP(i,j) = logical(1);
- end
- if isequal(name(13:15),'463')
- r463_dHP(i,j) = logical(1);
- end
- if isequal(name(13:15),'473')
- r473_dHP(i,j) = logical(1);
- end
- if isequal(name(13:15),'488')
- r488_dHP(i,j) = logical(1);
- end
- if isequal(name(13:15),'509')
- r509_dHP(i,j) = logical(1);
- end
- end
- end
- end
- SpatialInfo.dHP=ClusterInfo.Total_dHP_SpatialInfo(Active_dHP);
- SpatialInfo.dHP_Rat{1}=ClusterInfo.Total_dHP_SpatialInfo(Active_dHP & r448_dHP);
- SpatialInfo.dHP_Rat{2}=ClusterInfo.Total_dHP_SpatialInfo(Active_dHP & r459_dHP);
- SpatialInfo.dHP_Rat{3}=ClusterInfo.Total_dHP_SpatialInfo(Active_dHP & r463_dHP);
- SpatialInfo.dHP_Rat{4}=ClusterInfo.Total_dHP_SpatialInfo(Active_dHP & r473_dHP);
- SpatialInfo.dHP_Rat{5}=ClusterInfo.Total_dHP_SpatialInfo(Active_dHP & r488_dHP);
- SpatialInfo.dHP_Rat{6}=ClusterInfo.Total_dHP_SpatialInfo(Active_dHP & r509_dHP);
- SpatialInfo.iHP=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & iHP);
- SpatialInfo.iHP_Rat{1}=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & r448_iHP & iHP);
- SpatialInfo.iHP_Rat{2}=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & r459_iHP & iHP);
- SpatialInfo.iHP_Rat{3}=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & r463_iHP & iHP);
- SpatialInfo.iHP_Rat{4}=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & r473_iHP & iHP);
- SpatialInfo.iHP_Rat{5}=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & r488_iHP & iHP);
- SpatialInfo.iHP_Rat{6}=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & r509_iHP & iHP);
- SpatialInfo.vHP=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & vHP);
- SpatialInfo.vHP_Rat{1}=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & r448_iHP & vHP);
- SpatialInfo.vHP_Rat{2}=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & r459_iHP & vHP);
- SpatialInfo.vHP_Rat{3}=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & r463_iHP & vHP);
- SpatialInfo.vHP_Rat{4}=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & r473_iHP & vHP);
- SpatialInfo.vHP_Rat{5}=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & r488_iHP & vHP);
- SpatialInfo.vHP_Rat{6}=ClusterInfo.Total_iHP_SpatialInfo(Active_iHP & r509_iHP & vHP);
- fig=figure; hold on;
- fig.Position=[0 0 1000 500];
- clear Color;
- Color.color=2; Color.alpha=1;
- Jin_MeanSTE_Line(1,SpatialInfo.dHP,Color);
- for i=1:6
- mean(SpatialInfo.dHP_Rat{i})
- % plot(1, mean(SpatialInfo.dHP_Rat{i}),'r.')
- end
- Color.color=1;
- Jin_MeanSTE_Line(2,SpatialInfo.iHP,Color)
- for i=1:6
- % plot(2, mean(SpatialInfo.iHP_Rat{i}),'b.')
- end
- Color.color=3;
- Jin_MeanSTE_Line(3,SpatialInfo.vHP,Color)
- for i=1:6
- % plot(3, mean(SpatialInfo.vHP_Rat{i}),'g.')
- end
- % Statistical testing
- y.data0 = SpatialInfo.dHP;
- y.data1 = SpatialInfo.iHP;
- y.data2 = SpatialInfo.vHP;
- Y = [y.data0'; y.data1'; y.data2'];
- GROUP = [GetGroupingVar(y.data0,'dHP'); GetGroupingVar(y.data1,'iHP'); GetGroupingVar(y.data2,'vHP')];
- [Pvalue, result, ~] = Stat_ANOVA1(Y,GROUP);
- % % Multiple comparision between groups
- [~,p]=ttest2(y.data0, y.data1);
- [~,p]=ttest2(y.data0, y.data2);
- [~,p]=ttest2(y.data2, y.data1);
- %% Figure 1I, Place cell ratio
- Numb.PlaceCell_dHP=length(find(Active_dHP & SpatiallyModulated_dHP & (Information_dHP)));
- Numb.Total_dHP=length((Active_dHP));
- PlaceCellRatio.dHP= Numb.PlaceCell_dHP / Numb.Total_dHP;
- Numb.PlaceCell_dHP_448=length(find(Active_dHP & SpatiallyModulated_dHP & Information_dHP & r448_dHP));
- Numb.Total_dHP_448=length(find(r448_dHP));
- PlaceCellRatio.dHP_448= Numb.PlaceCell_dHP_448 / Numb.Total_dHP_448;
- Numb.PlaceCell_dHP_459=length(find(Active_dHP & SpatiallyModulated_dHP & Information_dHP & r459_dHP));
- Numb.Total_dHP_459=length(find(r459_dHP));
- PlaceCellRatio.dHP_459= Numb.PlaceCell_dHP_459 / Numb.Total_dHP_459;
- Numb.PlaceCell_dHP_463=length(find(Active_dHP & SpatiallyModulated_dHP & Information_dHP & r463_dHP));
- Numb.Total_dHP_463=length(find(r463_dHP));
- PlaceCellRatio.dHP_463= Numb.PlaceCell_dHP_463 / Numb.Total_dHP_463;
- Numb.PlaceCell_dHP_473=length(find(Active_dHP & SpatiallyModulated_dHP & Information_dHP & r473_dHP));
- Numb.Total_dHP_473=length(find(r473_dHP));
- PlaceCellRatio.dHP_473= Numb.PlaceCell_dHP_473 / Numb.Total_dHP_473;
- Numb.PlaceCell_dHP_488=length(find(Active_dHP & SpatiallyModulated_dHP & Information_dHP & r488_dHP));
- Numb.Total_dHP_488=length(find(r488_dHP));
- PlaceCellRatio.dHP_488= Numb.PlaceCell_dHP_488 / Numb.Total_dHP_488;
- Numb.PlaceCell_dHP_509=length(find(Active_dHP & SpatiallyModulated_dHP & Information_dHP & r509_dHP));
- Numb.Total_dHP_509=length(find(r509_dHP));
- PlaceCellRatio.dHP_509= Numb.PlaceCell_dHP_509 / Numb.Total_dHP_509;
- Numb.PlaceCell_iHP=length(find(Active_iHP & SpatiallyModulated_iHP & iHP & (Information_iHP)));
- Numb.Total_iHP=length(find(iHP));
- PlaceCellRatio.iHP= Numb.PlaceCell_iHP / Numb.Total_iHP;
- Numb.PlaceCell_iHP_448=length(find(Active_iHP & SpatiallyModulated_iHP & Information_iHP & iHP & r448_iHP));
- Numb.Total_iHP_448=length(find(r448_iHP& iHP));
- PlaceCellRatio.iHP_448= Numb.PlaceCell_iHP_448 / Numb.Total_iHP_448;
- Numb.PlaceCell_iHP_459=length(find(Active_iHP & SpatiallyModulated_iHP & Information_iHP & iHP & r459_iHP));
- Numb.Total_iHP_459=length(find(r459_iHP& iHP));
- PlaceCellRatio.iHP_459= Numb.PlaceCell_iHP_459 / Numb.Total_iHP_459;
- Numb.PlaceCell_iHP_463=length(find(Active_iHP & SpatiallyModulated_iHP & Information_iHP & iHP & r463_iHP));
- Numb.Total_iHP_463=length(find(r463_iHP& iHP));
- PlaceCellRatio.iHP_463= Numb.PlaceCell_iHP_463 / Numb.Total_iHP_463;
- Numb.PlaceCell_iHP_473=length(find(Active_iHP & SpatiallyModulated_iHP & Information_iHP & iHP & r473_iHP));
- Numb.Total_iHP_473=length(find(r473_iHP& iHP));
- PlaceCellRatio.iHP_473= Numb.PlaceCell_iHP_473 / Numb.Total_iHP_473;
- Numb.PlaceCell_iHP_488=length(find(Active_iHP & SpatiallyModulated_iHP & Information_iHP & iHP & r488_iHP));
- Numb.Total_iHP_488=length(find(r488_iHP& iHP));
- PlaceCellRatio.iHP_488= Numb.PlaceCell_iHP_488 / Numb.Total_iHP_488;
- Numb.PlaceCell_iHP_509=length(find(Active_iHP & SpatiallyModulated_iHP & Information_iHP & iHP & r509_iHP));
- Numb.Total_iHP_509=length(find(r509_iHP& iHP));
- PlaceCellRatio.iHP_509= Numb.PlaceCell_iHP_509 / Numb.Total_iHP_509;
- Numb.PlaceCell_vHP=length(find(Active_iHP & SpatiallyModulated_iHP & vHP & (Information_iHP)));
- Numb.Total_vHP=length(find(vHP));
- PlaceCellRatio.vHP= Numb.PlaceCell_vHP / Numb.Total_vHP;
- Numb.PlaceCell_vHP_448=length(find(Active_iHP & SpatiallyModulated_iHP & Information_iHP & vHP & r448_iHP));
- Numb.Total_vHP_448=length(find(r448_iHP& vHP));
- PlaceCellRatio.vHP_448= Numb.PlaceCell_vHP_448 / Numb.Total_vHP_448;
- Numb.PlaceCell_vHP_459=length(find(Active_iHP & SpatiallyModulated_iHP & Information_iHP & vHP & r459_iHP));
- Numb.Total_vHP_459=length(find(r459_iHP& vHP));
- PlaceCellRatio.vHP_459= Numb.PlaceCell_vHP_459 / Numb.Total_vHP_459;
- Numb.PlaceCell_vHP_463=length(find(Active_iHP & SpatiallyModulated_iHP & Information_iHP & vHP & r463_iHP));
- Numb.Total_vHP_463=length(find(r463_iHP& vHP));
- PlaceCellRatio.vHP_463= Numb.PlaceCell_vHP_463 / Numb.Total_vHP_463;
- Numb.PlaceCell_vHP_473=length(find(Active_iHP & SpatiallyModulated_iHP & Information_iHP & vHP & r473_iHP));
- Numb.Total_vHP_473=length(find(r473_iHP& vHP));
- PlaceCellRatio.vHP_473= Numb.PlaceCell_vHP_473 / Numb.Total_vHP_473;
- Numb.PlaceCell_vHP_488=length(find(Active_iHP & SpatiallyModulated_iHP & Information_iHP & vHP & r488_iHP));
- Numb.Total_vHP_488=length(find(r488_iHP& vHP));
- PlaceCellRatio.vHP_488= Numb.PlaceCell_vHP_488 / Numb.Total_vHP_488;
- Numb.PlaceCell_vHP_509=length(find(Active_iHP & SpatiallyModulated_iHP & Information_iHP & vHP & r509_iHP));
- Numb.Total_vHP_509=length(find(r509_iHP& vHP));
- PlaceCellRatio.vHP_509= Numb.PlaceCell_vHP_509 / Numb.Total_vHP_509;
- fig=figure;
- hold on;
- plot(1,PlaceCellRatio.dHP,'r.');
- plot(1,PlaceCellRatio.dHP_448,'ro');
- plot(1,PlaceCellRatio.dHP_459,'ro');
- plot(1,PlaceCellRatio.dHP_463,'ro');
- plot(1,PlaceCellRatio.dHP_473,'ro');
- plot(1,PlaceCellRatio.dHP_509,'ro');
- plot(2,PlaceCellRatio.iHP,'b.');
- plot(2,PlaceCellRatio.iHP_448,'bo');
- plot(2,PlaceCellRatio.iHP_459,'bo');
- plot(2,PlaceCellRatio.iHP_463,'bo');
- plot(2,PlaceCellRatio.iHP_473,'bo');
- plot(2,PlaceCellRatio.iHP_509,'bo');
- plot(3,PlaceCellRatio.vHP,'g.');
- plot(3,PlaceCellRatio.vHP_448,'go');
- plot(3,PlaceCellRatio.vHP_459,'go');
- plot(3,PlaceCellRatio.vHP_463,'go');
- plot(3,PlaceCellRatio.vHP_488,'go');
- plot(3,PlaceCellRatio.vHP_509,'go');
- xlim([0.5 3.5])
- % % Statistical testing
- [~,p,stat]=chi2cont([Numb.PlaceCell_dHP Numb.Total_dHP; Numb.PlaceCell_iHP Numb.Total_iHP; Numb.PlaceCell_vHP Numb.Total_vHP]);
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