clear all; load('ContextDecodingDay9.mat') clearvars -except idxs_of_SC_Cells All_LT_data_ms1 All_OF_data_ms1 All_LT_data_ms2 All_OF_data_ms2 All_LT_data_ms3 All_OF_data_ms3 ms1_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells<436); ms2_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells>435 & idxs_of_SC_Cells<=435+279); ms2_SCs=ms2_SCs-(435); ms3_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells>435+279 & idxs_of_SC_Cells<=435+279+304); ms3_SCs=ms3_SCs-(435+279); ms4_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells>435+279+304 & idxs_of_SC_Cells<=435+279+304+306); ms4_SCs=ms4_SCs-(435+279+304); num_bins=25; vel_threshold=4; LT_vel_threshold=0.1; LT_num_bins=70; make_plots=0; select_mouse=1; ms1string='D:/ACC Data/ACC/AllDays/635/'; ms2string='D:/ACC Data/ACC/AllDays/681/'; ms3string='D:/ACC Data/ACC/AllDays/691/'; ms4string='D:/ACC Data/ACC/AllDays/747/'; ltstring='/XYtotalspike3.csv'; ofstring='/XYtotalspike2.csv'; if select_mouse==1; setofcells=ms1_SCs; elseif select_mouse==2; setofcells=ms2_SCs; elseif select_mouse==3; setofcells=ms3_SCs; elseif select_mouse==4; setofcells=ms4_SCs; end; %idxs_of_SC_Cells=sort(idxs_of_SC_Cells,'ascend'); if select_mouse==1; LT_field_size=NaN(9,size(ms1_SCs,1));LT_field_num=NaN(9,size(ms1_SCs,1));LT_coverage=NaN(9,size(ms1_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms1_SCs,1));OF_field_num=NaN(9,size(ms1_SCs,1));OF_coverage=NaN(9,size(ms1_SCs,1)); elseif select_mouse==2; LT_field_size=NaN(9,size(ms2_SCs,1));LT_field_num=NaN(9,size(ms2_SCs,1));LT_coverage=NaN(9,size(ms2_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms2_SCs,1));OF_field_num=NaN(9,size(ms2_SCs,1));OF_coverage=NaN(9,size(ms2_SCs,1)); elseif select_mouse==3; LT_field_size=NaN(9,size(ms3_SCs,1));LT_field_num=NaN(9,size(ms3_SCs,1));LT_coverage=NaN(9,size(ms3_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms3_SCs,1));OF_field_num=NaN(9,size(ms3_SCs,1));OF_coverage=NaN(9,size(ms3_SCs,1)); elseif select_mouse==4; LT_field_size=NaN(9,size(ms4_SCs,1));LT_field_num=NaN(9,size(ms4_SCs,1));LT_coverage=NaN(9,size(ms4_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms4_SCs,1));OF_field_num=NaN(9,size(ms4_SCs,1));OF_coverage=NaN(9,size(ms4_SCs,1)); end; All_LT_data=NaN(9,69,length(setofcells)); All_OF_data=NaN(24,24,9,length(setofcells)); for cellnum=1:length(setofcells); cellnum raw_placemapOF=zeros(24,24,9);norm_placemapOF=zeros(24,24,9); raw_placemapLT=zeros(1,69,9);norm_placemapLT=zeros(1,69,9); for day_num=1:9; day_num day_var=sprintf('day%d', day_num); if select_mouse==1; OF_path_var=strcat(ms1string,day_var,ofstring); LT_path_var=strcat(ms1string,day_var,ltstring); elseif select_mouse==2; OF_path_var=strcat(ms2string,day_var,ofstring); LT_path_var=strcat(ms2string,day_var,ltstring); elseif select_mouse==3; OF_path_var=strcat(ms3string,day_var,ofstring); LT_path_var=strcat(ms3string,day_var,ltstring); elseif select_mouse==4; OF_path_var=strcat(ms4string,day_var,ofstring); LT_path_var=strcat(ms4string,day_var,ltstring); end; Ms1OF = readtable(OF_path_var); %Open Field Ms1OF = readtable(OF_path_var); x_posn=table2array(Ms1OF(:,2)); x_posn=smooth(x_posn,15); y_posn=table2array(Ms1OF(:,3)); y_posn=smooth(y_posn,15); Ms1OF=sparse(table2array(Ms1OF(1:end,6:end))); vel_cmsec=abs(diff(x_posn))+abs(diff(y_posn))*(1/0.05); vel_cmsec=smooth(vel_cmsec,30); still_periods=find(vel_cmsec0); [raw_placemapOF(:,:,day_num),XEDGES,YEDGES] = histcounts2(x_posn(spike_indxs),y_posn(spike_indxs),linspace(min(x_posn),max(x_posn),num_bins),linspace(min(y_posn),max(y_posn),num_bins)); norm_placemapOF(:,:,day_num)=raw_placemapOF(:,:,day_num)./Occupancy; norm_placemapOF(:,:,day_num)=imgaussfilt(norm_placemapOF(:,:,day_num),1); raw_placemapOF(isnan(raw_placemapOF))=0;norm_placemapOF(isnan(norm_placemapOF))=0; %Linear Track MsLT = readtable(LT_path_var); LT_xposn=MsLT.Var4; %LT_yposn=MsLT.Var3; LT_vel_cmsec=abs(diff(LT_xposn))*(1/0.05); LT_vel_cmsec=smooth(LT_vel_cmsec,30); Ms1LT=sparse(table2array(MsLT(1:end,6:end))); LT_still_periods=find(LT_vel_cmsec0); [raw_placemapLT(:,:,day_num),XEDGES,YEDGES] = histcounts(LT_xposn(spike_indxs),linspace(1,70,LT_num_bins)); norm_placemapLT(:,:,day_num)=raw_placemapLT(:,:,day_num)./LT_Occupancy; norm_placemapLT(:,:,day_num)=smooth(norm_placemapLT(:,:,day_num),5); norm_placemapLT(isnan(norm_placemapLT))=0;raw_placemapLT(isnan(raw_placemapLT))=0; end; All_LT_data(:,:,cellnum)=cat(1,norm_placemapLT(:,:,1),norm_placemapLT(:,:,2),norm_placemapLT(:,:,3),norm_placemapLT(:,:,4),norm_placemapLT(:,:,5),norm_placemapLT(:,:,6),norm_placemapLT(:,:,7),norm_placemapLT(:,:,8),norm_placemapLT(:,:,9)); All_OF_data(:,:,:,cellnum)=norm_placemapOF; if make_plots==1; figure; for fig_num=1:9; subplot(9,1,fig_num); imagesc(norm_placemapLT(:,:,fig_num));colormap jet; if max(max(norm_placemapLT))>0; clim([0 max(max(norm_placemapLT))]); else clim([0 1]); end; end; figure; for fig_num=1:9; subplot(1,9,fig_num) imagesc(norm_placemapOF(:,:,fig_num));axis square;colormap jet; if max(max(max(norm_placemapOF)))>0; clim([0 max(max(max(norm_placemapOF)))]); else clim([0 1]); end; end; end; end All_LT_data_ms1=All_LT_data; All_OF_data_ms1=All_OF_data; load('ContextDecodingDay9.mat') clearvars -except idxs_of_SC_Cells All_LT_data_ms1 All_OF_data_ms1 All_LT_data_ms2 All_OF_data_ms2 All_LT_data_ms3 All_OF_data_ms3 ms1_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells<436); ms2_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells>435 & idxs_of_SC_Cells<=435+279); ms2_SCs=ms2_SCs-(435); ms3_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells>435+279 & idxs_of_SC_Cells<=435+279+304); ms3_SCs=ms3_SCs-(435+279); ms4_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells>435+279+304 & idxs_of_SC_Cells<=435+279+304+306); ms4_SCs=ms4_SCs-(435+279+304); num_bins=25; vel_threshold=4; LT_vel_threshold=0.1; LT_num_bins=70; make_plots=0; select_mouse=2; ms1string='D:/ACC Data/ACC/AllDays/635/'; ms2string='D:/ACC Data/ACC/AllDays/681/'; ms3string='D:/ACC Data/ACC/AllDays/691/'; ms4string='D:/ACC Data/ACC/AllDays/747/'; ltstring='/XYtotalspike3.csv'; ofstring='/XYtotalspike2.csv'; if select_mouse==1; setofcells=ms1_SCs; elseif select_mouse==2; setofcells=ms2_SCs; elseif select_mouse==3; setofcells=ms3_SCs; elseif select_mouse==4; setofcells=ms4_SCs; end; %idxs_of_SC_Cells=sort(idxs_of_SC_Cells,'ascend'); if select_mouse==1; LT_field_size=NaN(9,size(ms1_SCs,1));LT_field_num=NaN(9,size(ms1_SCs,1));LT_coverage=NaN(9,size(ms1_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms1_SCs,1));OF_field_num=NaN(9,size(ms1_SCs,1));OF_coverage=NaN(9,size(ms1_SCs,1)); elseif select_mouse==2; LT_field_size=NaN(9,size(ms2_SCs,1));LT_field_num=NaN(9,size(ms2_SCs,1));LT_coverage=NaN(9,size(ms2_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms2_SCs,1));OF_field_num=NaN(9,size(ms2_SCs,1));OF_coverage=NaN(9,size(ms2_SCs,1)); elseif select_mouse==3; LT_field_size=NaN(9,size(ms3_SCs,1));LT_field_num=NaN(9,size(ms3_SCs,1));LT_coverage=NaN(9,size(ms3_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms3_SCs,1));OF_field_num=NaN(9,size(ms3_SCs,1));OF_coverage=NaN(9,size(ms3_SCs,1)); elseif select_mouse==4; LT_field_size=NaN(9,size(ms4_SCs,1));LT_field_num=NaN(9,size(ms4_SCs,1));LT_coverage=NaN(9,size(ms4_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms4_SCs,1));OF_field_num=NaN(9,size(ms4_SCs,1));OF_coverage=NaN(9,size(ms4_SCs,1)); end; All_LT_data=NaN(9,69,length(setofcells)); All_OF_data=NaN(24,24,9,length(setofcells)); for cellnum=1:length(setofcells); raw_placemapOF=zeros(24,24,9);norm_placemapOF=zeros(24,24,9); raw_placemapLT=zeros(1,69,9);norm_placemapLT=zeros(1,69,9); for day_num=1:9; day_var=sprintf('day%d', day_num); if select_mouse==1; OF_path_var=strcat(ms1string,day_var,ofstring); LT_path_var=strcat(ms1string,day_var,ltstring); elseif select_mouse==2; OF_path_var=strcat(ms2string,day_var,ofstring); LT_path_var=strcat(ms2string,day_var,ltstring); elseif select_mouse==3; OF_path_var=strcat(ms3string,day_var,ofstring); LT_path_var=strcat(ms3string,day_var,ltstring); elseif select_mouse==4; OF_path_var=strcat(ms4string,day_var,ofstring); LT_path_var=strcat(ms4string,day_var,ltstring); end; Ms1OF = readtable(OF_path_var); %Open Field Ms1OF = readtable(OF_path_var); x_posn=table2array(Ms1OF(:,2)); x_posn=smooth(x_posn,15); y_posn=table2array(Ms1OF(:,3)); y_posn=smooth(y_posn,15); Ms1OF=sparse(table2array(Ms1OF(1:end,6:end))); vel_cmsec=abs(diff(x_posn))+abs(diff(y_posn))*(1/0.05); vel_cmsec=smooth(vel_cmsec,30); still_periods=find(vel_cmsec0); [raw_placemapOF(:,:,day_num),XEDGES,YEDGES] = histcounts2(x_posn(spike_indxs),y_posn(spike_indxs),linspace(min(x_posn),max(x_posn),num_bins),linspace(min(y_posn),max(y_posn),num_bins)); norm_placemapOF(:,:,day_num)=raw_placemapOF(:,:,day_num)./Occupancy; norm_placemapOF(:,:,day_num)=imgaussfilt(norm_placemapOF(:,:,day_num),1); raw_placemapOF(isnan(raw_placemapOF))=0;norm_placemapOF(isnan(norm_placemapOF))=0; %Linear Track MsLT = readtable(LT_path_var); LT_xposn=MsLT.Var4; %LT_yposn=MsLT.Var3; LT_vel_cmsec=abs(diff(LT_xposn))*(1/0.05); LT_vel_cmsec=smooth(LT_vel_cmsec,30); Ms1LT=sparse(table2array(MsLT(1:end,6:end))); LT_still_periods=find(LT_vel_cmsec0); [raw_placemapLT(:,:,day_num),XEDGES,YEDGES] = histcounts(LT_xposn(spike_indxs),linspace(1,70,LT_num_bins)); norm_placemapLT(:,:,day_num)=raw_placemapLT(:,:,day_num)./LT_Occupancy; norm_placemapLT(:,:,day_num)=smooth(norm_placemapLT(:,:,day_num),5); norm_placemapLT(isnan(norm_placemapLT))=0;raw_placemapLT(isnan(raw_placemapLT))=0; end; All_LT_data(:,:,cellnum)=cat(1,norm_placemapLT(:,:,1),norm_placemapLT(:,:,2),norm_placemapLT(:,:,3),norm_placemapLT(:,:,4),norm_placemapLT(:,:,5),norm_placemapLT(:,:,6),norm_placemapLT(:,:,7),norm_placemapLT(:,:,8),norm_placemapLT(:,:,9)); All_OF_data(:,:,:,cellnum)=norm_placemapOF; if make_plots==1; figure; for fig_num=1:9; subplot(9,1,fig_num); imagesc(norm_placemapLT(:,:,fig_num));colormap jet; if max(max(norm_placemapLT))>0; clim([0 max(max(norm_placemapLT))]); else clim([0 1]); end; end; figure; for fig_num=1:9; subplot(1,9,fig_num) imagesc(norm_placemapOF(:,:,fig_num));axis square;colormap jet; if max(max(max(norm_placemapOF)))>0; clim([0 max(max(max(norm_placemapOF)))]); else clim([0 1]); end; end; end; end All_LT_data_ms2=All_LT_data; All_OF_data_ms2=All_OF_data; load('ContextDecodingDay9.mat') clearvars -except idxs_of_SC_Cells All_LT_data_ms1 All_OF_data_ms1 All_LT_data_ms2 All_OF_data_ms2 All_LT_data_ms3 All_OF_data_ms3 ms1_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells<436); ms2_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells>435 & idxs_of_SC_Cells<=435+279); ms2_SCs=ms2_SCs-(435); ms3_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells>435+279 & idxs_of_SC_Cells<=435+279+304); ms3_SCs=ms3_SCs-(435+279); ms4_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells>435+279+304 & idxs_of_SC_Cells<=435+279+304+306); ms4_SCs=ms4_SCs-(435+279+304); num_bins=25; vel_threshold=4; LT_vel_threshold=0.1; LT_num_bins=70; make_plots=0; select_mouse=3; ms1string='D:/ACC Data/ACC/AllDays/635/'; ms2string='D:/ACC Data/ACC/AllDays/681/'; ms3string='D:/ACC Data/ACC/AllDays/691/'; ms4string='D:/ACC Data/ACC/AllDays/747/'; ltstring='/XYtotalspike3.csv'; ofstring='/XYtotalspike2.csv'; if select_mouse==1; setofcells=ms1_SCs; elseif select_mouse==2; setofcells=ms2_SCs; elseif select_mouse==3; setofcells=ms3_SCs; elseif select_mouse==4; setofcells=ms4_SCs; end; %idxs_of_SC_Cells=sort(idxs_of_SC_Cells,'ascend'); if select_mouse==1; LT_field_size=NaN(9,size(ms1_SCs,1));LT_field_num=NaN(9,size(ms1_SCs,1));LT_coverage=NaN(9,size(ms1_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms1_SCs,1));OF_field_num=NaN(9,size(ms1_SCs,1));OF_coverage=NaN(9,size(ms1_SCs,1)); elseif select_mouse==2; LT_field_size=NaN(9,size(ms2_SCs,1));LT_field_num=NaN(9,size(ms2_SCs,1));LT_coverage=NaN(9,size(ms2_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms2_SCs,1));OF_field_num=NaN(9,size(ms2_SCs,1));OF_coverage=NaN(9,size(ms2_SCs,1)); elseif select_mouse==3; LT_field_size=NaN(9,size(ms3_SCs,1));LT_field_num=NaN(9,size(ms3_SCs,1));LT_coverage=NaN(9,size(ms3_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms3_SCs,1));OF_field_num=NaN(9,size(ms3_SCs,1));OF_coverage=NaN(9,size(ms3_SCs,1)); elseif select_mouse==4; LT_field_size=NaN(9,size(ms4_SCs,1));LT_field_num=NaN(9,size(ms4_SCs,1));LT_coverage=NaN(9,size(ms4_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms4_SCs,1));OF_field_num=NaN(9,size(ms4_SCs,1));OF_coverage=NaN(9,size(ms4_SCs,1)); end; All_LT_data=NaN(9,69,length(setofcells)); All_OF_data=NaN(24,24,9,length(setofcells)); for cellnum=1:length(setofcells); raw_placemapOF=zeros(24,24,9);norm_placemapOF=zeros(24,24,9); raw_placemapLT=zeros(1,69,9);norm_placemapLT=zeros(1,69,9); for day_num=1:9; day_var=sprintf('day%d', day_num); if select_mouse==1; OF_path_var=strcat(ms1string,day_var,ofstring); LT_path_var=strcat(ms1string,day_var,ltstring); elseif select_mouse==2; OF_path_var=strcat(ms2string,day_var,ofstring); LT_path_var=strcat(ms2string,day_var,ltstring); elseif select_mouse==3; OF_path_var=strcat(ms3string,day_var,ofstring); LT_path_var=strcat(ms3string,day_var,ltstring); elseif select_mouse==4; OF_path_var=strcat(ms4string,day_var,ofstring); LT_path_var=strcat(ms4string,day_var,ltstring); end; Ms1OF = readtable(OF_path_var); %Open Field Ms1OF = readtable(OF_path_var); x_posn=table2array(Ms1OF(:,2)); x_posn=smooth(x_posn,15); y_posn=table2array(Ms1OF(:,3)); y_posn=smooth(y_posn,15); Ms1OF=sparse(table2array(Ms1OF(1:end,6:end))); vel_cmsec=abs(diff(x_posn))+abs(diff(y_posn))*(1/0.05); vel_cmsec=smooth(vel_cmsec,30); still_periods=find(vel_cmsec0); [raw_placemapOF(:,:,day_num),XEDGES,YEDGES] = histcounts2(x_posn(spike_indxs),y_posn(spike_indxs),linspace(min(x_posn),max(x_posn),num_bins),linspace(min(y_posn),max(y_posn),num_bins)); norm_placemapOF(:,:,day_num)=raw_placemapOF(:,:,day_num)./Occupancy; norm_placemapOF(:,:,day_num)=imgaussfilt(norm_placemapOF(:,:,day_num),1); raw_placemapOF(isnan(raw_placemapOF))=0;norm_placemapOF(isnan(norm_placemapOF))=0; %Linear Track MsLT = readtable(LT_path_var); LT_xposn=MsLT.Var4; %LT_yposn=MsLT.Var3; LT_vel_cmsec=abs(diff(LT_xposn))*(1/0.05); LT_vel_cmsec=smooth(LT_vel_cmsec,30); Ms1LT=sparse(table2array(MsLT(1:end,6:end))); LT_still_periods=find(LT_vel_cmsec0); [raw_placemapLT(:,:,day_num),XEDGES,YEDGES] = histcounts(LT_xposn(spike_indxs),linspace(1,70,LT_num_bins)); norm_placemapLT(:,:,day_num)=raw_placemapLT(:,:,day_num)./LT_Occupancy; norm_placemapLT(:,:,day_num)=smooth(norm_placemapLT(:,:,day_num),5); norm_placemapLT(isnan(norm_placemapLT))=0;raw_placemapLT(isnan(raw_placemapLT))=0; end; All_LT_data(:,:,cellnum)=cat(1,norm_placemapLT(:,:,1),norm_placemapLT(:,:,2),norm_placemapLT(:,:,3),norm_placemapLT(:,:,4),norm_placemapLT(:,:,5),norm_placemapLT(:,:,6),norm_placemapLT(:,:,7),norm_placemapLT(:,:,8),norm_placemapLT(:,:,9)); All_OF_data(:,:,:,cellnum)=norm_placemapOF; if make_plots==1; figure; for fig_num=1:9; subplot(9,1,fig_num); imagesc(norm_placemapLT(:,:,fig_num));colormap jet; if max(max(norm_placemapLT))>0; clim([0 max(max(norm_placemapLT))]); else clim([0 1]); end; end; figure; for fig_num=1:9; subplot(1,9,fig_num) imagesc(norm_placemapOF(:,:,fig_num));axis square;colormap jet; if max(max(max(norm_placemapOF)))>0; clim([0 max(max(max(norm_placemapOF)))]); else clim([0 1]); end; end; end; end All_LT_data_ms3=All_LT_data; All_OF_data_ms3=All_OF_data; load('ContextDecodingDay9.mat') clearvars -except idxs_of_SC_Cells All_LT_data_ms1 All_OF_data_ms1 All_LT_data_ms2 All_OF_data_ms2 All_LT_data_ms3 All_OF_data_ms3 ms1_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells<436); ms2_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells>435 & idxs_of_SC_Cells<=435+279); ms2_SCs=ms2_SCs-(435); ms3_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells>435+279 & idxs_of_SC_Cells<=435+279+304); ms3_SCs=ms3_SCs-(435+279); ms4_SCs=idxs_of_SC_Cells(idxs_of_SC_Cells>435+279+304 & idxs_of_SC_Cells<=435+279+304+306); ms4_SCs=ms4_SCs-(435+279+304); num_bins=25; vel_threshold=4; LT_vel_threshold=0.1; LT_num_bins=70; make_plots=0; select_mouse=4; ms1string='D:/ACC Data/ACC/AllDays/635/'; ms2string='D:/ACC Data/ACC/AllDays/681/'; ms3string='D:/ACC Data/ACC/AllDays/691/'; ms4string='D:/ACC Data/ACC/AllDays/747/'; ltstring='/XYtotalspike3.csv'; ofstring='/XYtotalspike2.csv'; if select_mouse==1; setofcells=ms1_SCs; elseif select_mouse==2; setofcells=ms2_SCs; elseif select_mouse==3; setofcells=ms3_SCs; elseif select_mouse==4; setofcells=ms4_SCs; end; %idxs_of_SC_Cells=sort(idxs_of_SC_Cells,'ascend'); if select_mouse==1; LT_field_size=NaN(9,size(ms1_SCs,1));LT_field_num=NaN(9,size(ms1_SCs,1));LT_coverage=NaN(9,size(ms1_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms1_SCs,1));OF_field_num=NaN(9,size(ms1_SCs,1));OF_coverage=NaN(9,size(ms1_SCs,1)); elseif select_mouse==2; LT_field_size=NaN(9,size(ms2_SCs,1));LT_field_num=NaN(9,size(ms2_SCs,1));LT_coverage=NaN(9,size(ms2_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms2_SCs,1));OF_field_num=NaN(9,size(ms2_SCs,1));OF_coverage=NaN(9,size(ms2_SCs,1)); elseif select_mouse==3; LT_field_size=NaN(9,size(ms3_SCs,1));LT_field_num=NaN(9,size(ms3_SCs,1));LT_coverage=NaN(9,size(ms3_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms3_SCs,1));OF_field_num=NaN(9,size(ms3_SCs,1));OF_coverage=NaN(9,size(ms3_SCs,1)); elseif select_mouse==4; LT_field_size=NaN(9,size(ms4_SCs,1));LT_field_num=NaN(9,size(ms4_SCs,1));LT_coverage=NaN(9,size(ms4_SCs,1)); OF_field_size_in_cm=NaN(9,size(ms4_SCs,1));OF_field_num=NaN(9,size(ms4_SCs,1));OF_coverage=NaN(9,size(ms4_SCs,1)); end; All_LT_data=NaN(9,69,length(setofcells)); All_OF_data=NaN(24,24,9,length(setofcells)); for cellnum=1:length(setofcells); raw_placemapOF=zeros(24,24,9);norm_placemapOF=zeros(24,24,9); raw_placemapLT=zeros(1,69,9);norm_placemapLT=zeros(1,69,9); for day_num=1:9; day_var=sprintf('day%d', day_num); if select_mouse==1; OF_path_var=strcat(ms1string,day_var,ofstring); LT_path_var=strcat(ms1string,day_var,ltstring); elseif select_mouse==2; OF_path_var=strcat(ms2string,day_var,ofstring); LT_path_var=strcat(ms2string,day_var,ltstring); elseif select_mouse==3; OF_path_var=strcat(ms3string,day_var,ofstring); LT_path_var=strcat(ms3string,day_var,ltstring); elseif select_mouse==4; OF_path_var=strcat(ms4string,day_var,ofstring); LT_path_var=strcat(ms4string,day_var,ltstring); end; Ms1OF = readtable(OF_path_var); %Open Field Ms1OF = readtable(OF_path_var); x_posn=table2array(Ms1OF(:,2)); x_posn=smooth(x_posn,15); y_posn=table2array(Ms1OF(:,3)); y_posn=smooth(y_posn,15); Ms1OF=sparse(table2array(Ms1OF(1:end,6:end))); vel_cmsec=abs(diff(x_posn))+abs(diff(y_posn))*(1/0.05); vel_cmsec=smooth(vel_cmsec,30); still_periods=find(vel_cmsec0); [raw_placemapOF(:,:,day_num),XEDGES,YEDGES] = histcounts2(x_posn(spike_indxs),y_posn(spike_indxs),linspace(min(x_posn),max(x_posn),num_bins),linspace(min(y_posn),max(y_posn),num_bins)); norm_placemapOF(:,:,day_num)=raw_placemapOF(:,:,day_num)./Occupancy; norm_placemapOF(:,:,day_num)=imgaussfilt(norm_placemapOF(:,:,day_num),1); raw_placemapOF(isnan(raw_placemapOF))=0;norm_placemapOF(isnan(norm_placemapOF))=0; %Linear Track MsLT = readtable(LT_path_var); LT_xposn=MsLT.Var4; %LT_yposn=MsLT.Var3; LT_vel_cmsec=abs(diff(LT_xposn))*(1/0.05); LT_vel_cmsec=smooth(LT_vel_cmsec,30); Ms1LT=sparse(table2array(MsLT(1:end,6:end))); LT_still_periods=find(LT_vel_cmsec0); [raw_placemapLT(:,:,day_num),XEDGES,YEDGES] = histcounts(LT_xposn(spike_indxs),linspace(1,70,LT_num_bins)); norm_placemapLT(:,:,day_num)=raw_placemapLT(:,:,day_num)./LT_Occupancy; norm_placemapLT(:,:,day_num)=smooth(norm_placemapLT(:,:,day_num),5); norm_placemapLT(isnan(norm_placemapLT))=0;raw_placemapLT(isnan(raw_placemapLT))=0; end; All_LT_data(:,:,cellnum)=cat(1,norm_placemapLT(:,:,1),norm_placemapLT(:,:,2),norm_placemapLT(:,:,3),norm_placemapLT(:,:,4),norm_placemapLT(:,:,5),norm_placemapLT(:,:,6),norm_placemapLT(:,:,7),norm_placemapLT(:,:,8),norm_placemapLT(:,:,9)); All_OF_data(:,:,:,cellnum)=norm_placemapOF; if make_plots==1; figure; for fig_num=1:9; subplot(9,1,fig_num); imagesc(norm_placemapLT(:,:,fig_num));colormap jet; if max(max(norm_placemapLT))>0; clim([0 max(max(norm_placemapLT))]); else clim([0 1]); end; end; figure; for fig_num=1:9; subplot(1,9,fig_num) imagesc(norm_placemapOF(:,:,fig_num));axis square;colormap jet; if max(max(max(norm_placemapOF)))>0; clim([0 max(max(max(norm_placemapOF)))]); else clim([0 1]); end; end; end; end All_LT_data_ms4=All_LT_data; All_OF_data_ms4=All_OF_data; clearvars -except All_LT_data_ms1 All_OF_data_ms1 All_LT_data_ms2 All_OF_data_ms2 ... All_LT_data_ms3 All_OF_data_ms3 All_LT_data_ms4 All_OF_data_ms4 save 'SCCellMaps.mat' mouseLT=All_LT_data_ms4; mouseOF=All_OF_data_ms4; for cellnum=1:size(All_LT_data_ms4,3); figure(1); for fig_num=1:9; subplot(9,1,fig_num); imagesc(mouseLT(fig_num,:,cellnum));colormap jet; if max(max(mouseLT(fig_num,:,cellnum)))>0; caxis([0 max(max(mouseLT(fig_num,:,cellnum)))]); else caxis([0 1]); end; end; saveas(gcf,['LTmaps_cell' num2str(cellnum) '.eps']); close all; figure(2); for fig_num=1:9; subplot(1,9,fig_num) imagesc(mouseOF(:,:,fig_num,cellnum));axis square;colormap jet; if max(max(max(mouseOF(:,:,fig_num,cellnum))))>0; caxis([0 max(max(max(mouseOF(:,:,fig_num,cellnum))))]); else caxis([0 1]); end; end; saveas(gcf,['OFmaps_cell' num2str(cellnum) '.eps']); close all; end; % % % mouseLT=All_LT_data_ms4; % mouseOF=All_OF_data_ms4; % % for cellnum=1:size(All_LT_data_ms4,3); % figure; % cmxlt=max(max(mouseLT(:,:,cellnum))); % cmxof=max(max(max(mouseOF(:,:,:,cellnum)))); % % % a = subplot(9,2,2); imagesc(mouseLT(1,:,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % b = subplot(9,2,4); imagesc(mouseLT(2,:,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % c = subplot(9,2,6); imagesc(mouseLT(3,:,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % d = subplot(9,2,8); imagesc(mouseLT(4,:,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % e = subplot(9,2,10); imagesc(mouseLT(5,:,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % f = subplot(9,2,12); imagesc(mouseLT(6,:,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % g = subplot(9,2,14); imagesc(mouseLT(7,:,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % h = subplot(9,2,16); imagesc(mouseLT(8,:,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % i = subplot(9,2,18); imagesc(mouseLT(9,:,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % a2 = subplot(9,2,1); imagesc(mouseOF(:,:,1,cellnum));colormap jet;axis off;caxis([0 cmxlt]);%scaled to LT % b2 = subplot(9,2,3); imagesc(mouseOF(:,:,2,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % c2 = subplot(9,2,5); imagesc(mouseOF(:,:,3,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % d2 = subplot(9,2,7); imagesc(mouseOF(:,:,4,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % e2 = subplot(9,2,9); imagesc(mouseOF(:,:,5,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % f2 = subplot(9,2,11); imagesc(mouseOF(:,:,6,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % g2 = subplot(9,2,13); imagesc(mouseOF(:,:,7,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % h2 = subplot(9,2,15); imagesc(mouseOF(:,:,8,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % i2 = subplot(9,2,17); imagesc(mouseOF(:,:,9,cellnum));colormap jet;axis off;caxis([0 cmxlt]); % set(a, 'Position', [0.25 0.91 .7 .08]); % set(b, 'Position', [0.25 0.81 .7 .08]); % set(c, 'Position', [0.25 0.71 .7 .08]); % set(d, 'Position', [0.25 0.61 .7 .08]); % set(e, 'Position', [0.25 0.51 .7 .08]); % set(f, 'Position', [0.25 0.41 .7 .08]); % set(g, 'Position', [0.25 0.31 .7 .08]); % set(h, 'Position', [0.25 0.21 .7 .08]); % set(i, 'Position', [0.25 0.11 .7 .08]); % % set(a2, 'Position', [0.1 0.91 .08 .08]); % set(b2, 'Position', [0.1 0.81 .08 .08]); % set(c2, 'Position', [0.1 0.71 .08 .08]); % set(d2, 'Position', [0.1 0.61 .08 .08]); % set(e2, 'Position', [0.1 0.51 .08 .08]); % set(f2, 'Position', [0.1 0.41 .08 .08]); % set(g2, 'Position', [0.1 0.31 .08 .08]); % set(h2, 'Position', [0.1 0.21 .08 .08]); % set(i2, 'Position', [0.1 0.11 .08 .08]);axis off; % % % saveas(gcf,['SCmaps_cell' num2str(cellnum) '.png']); % close all; end;