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neon_fullscreen_statistics_all_v2.m
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neon_fullscreen_statistics_all_v2.m
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%%%% statistics
%% parameters
close all
clear
tic
data_folder = 'D:\matwork\data\higher_vision';
mouse_numbers = [164 185 335 336 337 405 407];
% mouse_numbers = [405 407];
session_name = 'neon';
session_num = 2; %for neon
plot_raster = 0; %%% plot raster for preferred angle?
plot_power = 0; %%% plot power spectrum
stim_angle = [0 45 90 135 180 225 270 315];
stim_type = [1 2];
neon_type = [1 2 3];
Ncond = length(stim_type)*length(stim_angle)*length(neon_type);
angle_loc = reshape(1:Ncond,length(stim_angle),length(stim_type)*length(neon_type));
area_names = {'V1';'LM';'LI';'LL'};
ave_act = [];
ave_act2 = [];
phase_angle = [];
first_comp = [];
zero_comp = [];
f1f0 = [];
f2f1f0 = [];
f2f1 = [];
latency4 = [];
latency2 = [];
preferred_ang = [];
exited = [];
cid = [];
OSI = [];
DSI = [];
ave_latency = [];
pv_simplicity = [];
h_simplicity = [];
S_S = [];
Depths = [];
TPlatency = [];
PTratio = [];
F1_dominant = [];
RF_size = [];
RF_loc = [];
RF_label = [];
RF_size_area = [];
Cell_area = [];
tag = cell(2,1);
dummyAllneuron = 0;
for mouse_number=1:length(mouse_numbers)
%% getting forders for analysis
%%% Kilosort foldels
mouse = ['M',num2str(mouse_numbers(mouse_number))];
KS_dirs = cell(1,1);
folders = dir(data_folder);
j=1;
for i=1:length(folders)
if length(folders(i).name)>4 && strcmp(folders(i).name(1:4),mouse)
KS_dirs{j,1}=fullfile(data_folder,folders(i).name);
j=j+1;
end
end
%%
for day=1:length(KS_dirs) %% loop for different days
%% loading
inputfile_stm = [KS_dirs{day},KS_dirs{day}(end-15:end),'_stimulus_time.mat'];
load(inputfile_stm)
load([KS_dirs{day},'\',session_name,'_spike_data.mat'])
load([KS_dirs{day},'\spike_Feature.mat'])
%% asigning previously calculated variables in each day
tf = stimulus_TemporalFreq{session_num}; % temporal frequency (cycle/s)
cycles = stimulus_cycles{session_num};
sourc_folder = fullfile(KS_dirs{day},session_name);
spikes = spike_data.spikes;
pdfs = spike_data.pdfs;
RFs = spike_data.RFs;
dx = spike_data.dx;
smoothed_pdfs = spike_data.smoothed_pdf;
xp = spike_data.xp;
stim_len = spike_data.stim_len;
%surround_sup = spike_data.surround_suppression;
evoked_cids = cell2mat(spike_data.evoked_cids);
evoked_ind = ismember(sp.cids,evoked_cids);
depth = sp.clusDepths(evoked_ind);
RF_cell = f_RF_select(KS_dirs{day},depth,0,'RF');
%% concatenating
Depths = vertcat(Depths,depth);
TPlatency = vertcat(TPlatency,sp.clusTPlatency(evoked_ind)./30);
PTratio = vertcat(PTratio,sp.clusTPratio(evoked_ind));
cid = vertcat(cid,cell2mat(spike_data.evoked_cids)'); %#ok<*AGROW>
ave_latency = vertcat(ave_latency,cell2mat(spike_data.average_latency)');
num_loc = regexp(KS_dirs{day},'_+[0-9]');
tarikh = ['D',KS_dirs{day}(num_loc(3)+1:num_loc(3)+2),'/',KS_dirs{day}(num_loc(2)+1:num_loc(2)+2)];
RF_size = vertcat(RF_size,RF_cell.RF_size);
RF_loc = vertcat(RF_loc,RF_cell.RF_loc);
RF_label = vertcat(RF_label,RF_cell.RF_label);
RF_size_area = vertcat(RF_size_area,RF_cell.RF_area);
Cell_area = vertcat(Cell_area,RF_cell.area); %% area: 1 = V1, 2 = LM , 3 = LI , 4 = LL
[~, onset_ind] = min(abs(xp));
[~,offset_ind] = min(abs(xp-stim_len));
[~,halfset_ind] = min(abs(xp-stim_len/2));
Nc = length(pdfs); %number of clusters
%% preallocating some intermediate variables
ave_activity_cond = zeros(Nc,6);
ave_activity_cond2 = zeros(Nc,6);
phase_angle_cond = zeros(Nc,6);
first_comp_cond = nan(Nc,6);
zero_comp_cond = nan(Nc,6);
f1f0_cond = nan(Nc,6);
f2f1f0_cond = nan(Nc,6);
f2f1_cond = nan(Nc,6);
latency_cond4 = nan(Nc,6);
latency_cond3 = nan(Nc,6);
response_type = zeros(Nc,1);
dominant_f1 = zeros(Nc,1);
%% some params
transient_time = 150; %in ms to exclude the transient component
transient_nbins= transient_time/(dx*1000);
bin_size=10;
FS=1/(dx*bin_size); % freq. of sampling in PSTH
%%single neuron calculation
for neuron=1:Nc %%%loop over clusters in one day
if plot_power
neuron_name = [mouse,'_D',KS_dirs{day}(num_loc(3)+1:num_loc(3)+2),'-',KS_dirs{day}(num_loc(2)+1:num_loc(2)+2),'_ID',num2str(spike_data.evoked_cids{neuron})];
PS=figure('visible','off');
cond_names = {'NCS', 'LDG','NCS+ring','NCS+squar','NCS+circle','LDG+circle'};
cond_loc_plot = [1 2 6 5 3 4];
end
dummyAllneuron = dummyAllneuron+1;
tag{dummyAllneuron} = [mouse,tarikh,'id',num2str(spike_data.evoked_cids{neuron})];
spike = spikes{neuron};
Pdf = pdfs{neuron};
Pdf2 = pdfs{neuron};
RF = RFs{neuron};
smoothed_pdf = smoothed_pdfs{neuron};
%% preferred_angle and OSI DSI
cond_preferred_angle = nan(1,6);
cond_preferred_ind = nan(1,6);
osi = nan(1,6);
dsi = nan(1,6);
psth_locs = nan(1,6);
for ip=1:6
Report=0;
[cond_preferred_angle(ip),cond_preferred_ind(ip),osi(ip),dsi(ip)]=f_find_preferred6_cond(spike_data,stim_angle,angle_loc,onset_ind,offset_ind,ip,KS_dirs{day},neuron,Report);
psth_locs(ip)=angle_loc(cond_preferred_ind(ip),ip);
end
OSI = [OSI;osi];
DSI = [DSI;dsi];
preferred_ang=[preferred_ang;cond_preferred_angle];
%% pre_stimulus_baseline
pre_stimulus_baseline=mean(mean(Pdf(psth_locs,1:onset_ind-1)));
if pre_stimulus_baseline
Pdf=(Pdf-pre_stimulus_baseline);%./pre_stimulus_baseline; %% normalizing psth by pre_stimulus_baseline
end
pre_stimulus_baseline_smooth=mean(mean(smoothed_pdf(psth_locs,1:onset_ind-1)));
if pre_stimulus_baseline_smooth
smoothed_pdf=(smoothed_pdf-pre_stimulus_baseline_smooth);%./pre_stimulus_baseline_smooth; %% normalizing psth by pre_stimulus_baseline
end
%% conditional calculations like ave_activity, phase and latency
for cond=1:length(psth_locs) %%6 condition (1:neon 2:phy 3:ring block (ctrl) 4:squar block 5:circle 6:phy+circle) of preferred angle
ave_activity_cond(neuron,cond) = mean(Pdf(psth_locs(cond),onset_ind:offset_ind));
ave_activity_cond2(neuron,cond) = mean(Pdf2(psth_locs(cond),onset_ind:offset_ind));
cond_smoothed_pdf = smoothed_pdf(psth_locs(cond),onset_ind+transient_nbins-1:offset_ind+transient_nbins);
s1 =length(cond_smoothed_pdf); m = s1 - mod(s1, bin_size);
cond_smoothed_pdf=mean(reshape(cond_smoothed_pdf(1:m),bin_size,[]));
%% phase and modulation calculation
L=length(cond_smoothed_pdf);
freq=FS*(0:(L/2))/L;%%0:FS/length(x):FS-1;
[~,f1_ind] = min(abs(freq-tf));
[~,f2_ind] = min(abs(freq-tf*2));
f = fft(cond_smoothed_pdf)/L;
phase_angle_cond(neuron,cond)= angle(f(f1_ind));
f1 = abs(f(f1_ind))*2;
f2 = abs(f(f2_ind))*2;
f0=f(1);
first_comp_cond(neuron,cond) = f1;
zero_comp_cond(neuron,cond) = f0;
f1f0_cond(neuron,cond) = (f1-f0)/(f0+f1);
f2f1f0_cond(neuron,cond) = (f2+f1-f0)/(f0+f2+f1);
f2f1_cond(neuron,cond) = (f2-f1)/(f2+f1);
f(1)=0; f=abs(f);f=f(1:floor(L/2)+1);f(2:end-1)=2*f(2:end-1);
if cond==2
ff=fft(cond_smoothed_pdf-mean(cond_smoothed_pdf));ff=abs(ff/L);ff=ff(1:floor(L/2)+1);ff(2:end-1)=2*ff(2:end-1);
[~ ,domominat_loc]=max(ff);
if domominat_loc==f1_ind
dominant_f1(neuron)=1;
end
end
%% power spectrum plot
if plot_power
subplot(3,2,cond_loc_plot(cond))
plot(freq,f)
hold on
plot(f1_ind-1,f1,'r*')
plot((f2_ind-1),f2,'g*')
title([cond_names{cond},' f1f0=',num2str(f1f0_cond(neuron,cond)),',f1f2=',num2str(f2f1_cond(neuron,cond))])
xlim([0,25])
xlabel('frequency (Hz)')
ylabel('power')
end
%% conditional response latency
cond_RF = RF(psth_locs(cond),:);
n=4; %number of merging bins
cond_RF4=cond_RF;
s1=length(cond_RF4);
m = s1 - mod(s1, n);
cond_RF4=reshape(cond_RF4(1:m),n,[]);
cond_RF4=sum(cond_RF4);
teta = f_resp_latency(cond_RF4,floor(onset_ind/n),0,floor(offset_ind/(n)));
if ~isempty(teta)
latency_cond4(neuron,cond)=teta*n;
end
cond_RF3 = movsum(cond_RF,3);
teta = f_resp_latency(cond_RF3,onset_ind,0,offset_ind);
if ~isempty(teta)
latency_cond3(neuron,cond)=teta;
end
end
if plot_power
saveas(PS,[data_folder,'/PS_',neuron_name,'.png'])
close(PS)
end
if mean(ave_activity_cond(neuron,:))>=0
response_type(neuron)=1; %%%"Excited";
end
%% plot raster for preferred angle
if plot_raster
f_neon6_plot_pref_raster(KS_dirs{day},cond_preferred_angle,psth_locs,spike_data,neuron,latency_cond4(neuron,:),latency_cond3(neuron,:),bin_size,area_names{RF_cell.area(neuron)},session_name,f1f0_cond(neuron,:)) %#ok<*UNRCH>
end
%% simplicity T-test
% tag{dummy_all_neuron}
phy_smoothed_pdf = (abs(smoothed_pdf(psth_locs(2),onset_ind+transient_nbins-1:offset_ind)));
xp_phy = xp(onset_ind+transient_nbins-1:offset_ind);
[~,h_simpl] = f_simplicity_test(phy_smoothed_pdf, xp_phy, spike, psth_locs);
h_simplicity = [h_simplicity;h_simpl];
end
ave_act = vertcat(ave_act,ave_activity_cond); %ave_act is the mean value of reduced responce (pre-stim reduced)
ave_act2 = vertcat(ave_act2,ave_activity_cond2); %ave_act2 is the mean value of raw Firing rate
exited = vertcat(exited,response_type);
phase_angle = vertcat(phase_angle,phase_angle_cond);
first_comp = vertcat(first_comp,first_comp_cond);
zero_comp = vertcat(zero_comp,zero_comp_cond);
f1f0 = vertcat(f1f0,f1f0_cond);
f2f1f0 = vertcat(f2f1f0,f2f1f0_cond);
f2f1 = vertcat(f2f1,f2f1_cond);
latency4 = vertcat(latency4,latency_cond4);
latency2 = vertcat(latency2,latency_cond3);
F1_dominant = vertcat(F1_dominant,dominant_f1);
%% surround_suppression
SR_day=NaN(length(evoked_cids),1);
% for isr=1:length(evoked_cids)
% id_loc=ismember(surround_sup(1,:),evoked_cids(isr));
% if sum(id_loc)~=0
% SR_day(isr)=surround_sup(2,id_loc);
% end
% end
SR_day(SR_day<-1)=nan;
S_S = vertcat(S_S,SR_day);
end
end
phase_diff = rad2deg(angdiff(phase_angle(:,1),phase_angle(:,2)));
twopi_phase_diff = rad2deg(wrapTo2Pi((phase_angle(:,1)-phase_angle(:,2))));
norm_rel_amp_f1 = (first_comp(:,1)-first_comp(:,2))./(first_comp(:,1)+first_comp(:,2));
ave_IGR2 = ((ave_act2(:,1))-(ave_act2(:,2)))./((ave_act2(:,1))+(ave_act2(:,2))); %ave_act2 is the mean value of raw Firing rate
ave_IGR1 = (abs(ave_act(:,1))-abs(ave_act(:,2)))./(abs(ave_act(:,1))+abs(ave_act(:,2))); %ave_act is the mean value of reduced responce (pre-stim reduced)
%intersection_point = f_intersect_gauss2_for_hist_v2(TPlatency,1000,.4,.5,1); %inputs(vect,Nbin,aa,bb,report) /sugest an in terval for the intersection [aa,bb]
intersection_point = 0.5021;
Icell_ind = TPlatency<=intersection_point;
how_fast = 80; %(ms)
fast_phy = latency4(:,2) <=how_fast;
fast_neon = latency4(:,1) <=how_fast;
fast_phy_neon = logical(fast_neon.*fast_phy);
shifted_ind = abs(phase_diff) >=120;
%% neurons type based on being evoked in different condition
evoke_phy_ind = ~isnan(latency2(:,2));
evoke_neon_ind = ~isnan(latency2(:,1));
both_evoked = evoke_neon_ind & evoke_phy_ind;
only_phy = evoke_phy_ind & ~evoke_neon_ind;
only_neon = ~evoke_phy_ind & evoke_neon_ind;
excited_idx = logical(exited);
evoked_idx = true(length(exited),1);
LDG_excited_idx = evoke_phy_ind & ave_act(:,2)>=0;
both_excited_idx = both_evoked & ave_act(:,2)>=0;
com_ldg_excited = LDG_excited_idx & f1f0(:,2)<=0;
evoked_any = (sum(~isnan(latency2)')~=0)';
evoked_V1_ind = Cell_area==1 & ~isnan(latency2);
evoked_lm_ind = Cell_area==2 & ~isnan(latency2);
evoked_li_ind = Cell_area==3 & ~isnan(latency2);
evoked_ll_ind = Cell_area==4 & ~isnan(latency2);
total_v1_evoked = sum (evoked_any & Cell_area==1);
total_lm_evoked = sum (evoked_any & Cell_area==2);
total_li_evoked = sum (evoked_any & Cell_area==3);
total_ll_evoked = sum (evoked_any & Cell_area==4);
NCS_V1_evoked = sum(evoked_V1_ind(:,1))/total_v1_evoked;
NCS_lm_evoked = sum(evoked_lm_ind(:,1))/total_lm_evoked;
NCS_li_evoked = sum(evoked_li_ind(:,1))/total_li_evoked;
NCS_ll_evoked = sum(evoked_ll_ind(:,1))/total_ll_evoked;
NCS_evoked_percent=[NCS_V1_evoked NCS_lm_evoked NCS_li_evoked NCS_ll_evoked]*100;
ldg_V1_evoked = sum(evoked_V1_ind(:,2))/total_v1_evoked;
ldg_lm_evoked = sum(evoked_lm_ind(:,2))/total_lm_evoked;
ldg_li_evoked = sum(evoked_li_ind(:,2))/total_li_evoked;
ldg_ll_evoked = sum(evoked_ll_ind(:,2))/total_ll_evoked;
LDG_evoked_percent=[ldg_V1_evoked ldg_lm_evoked ldg_li_evoked ldg_ll_evoked]*100;
sqr_V1_evoked = sum(evoked_V1_ind(:,4))/total_v1_evoked;
sqr_lm_evoked = sum(evoked_lm_ind(:,4))/total_lm_evoked;
sqr_li_evoked = sum(evoked_li_ind(:,4))/total_li_evoked;
sqr_ll_evoked = sum(evoked_ll_ind(:,4))/total_ll_evoked;
SQR_evoked_percent=[sqr_V1_evoked sqr_lm_evoked sqr_li_evoked sqr_ll_evoked]*100;
crcl_V1_evoked = sum(evoked_V1_ind(:,5))/total_v1_evoked;
crcl_lm_evoked = sum(evoked_lm_ind(:,5))/total_lm_evoked;
crcl_li_evoked = sum(evoked_li_ind(:,5))/total_li_evoked;
crcl_ll_evoked = sum(evoked_ll_ind(:,5))/total_ll_evoked;
CRCL_evoked_percent = [crcl_V1_evoked crcl_lm_evoked crcl_li_evoked crcl_ll_evoked]*100;
evoked_percent = [NCS_evoked_percent; LDG_evoked_percent;SQR_evoked_percent;CRCL_evoked_percent];
%% edge selectives
edge_selective = f2f1>=0 & f2f1f0>=0 & ~isnan(latency4);
sum(edge_selective)
neon_edge=edge_selective(:,1) & exited;
%% saving
stat_data.ave_act = ave_act;
stat_data.ave_act2 = ave_act2;
stat_data.phase_angle = phase_angle;
stat_data.latency4 = latency4;
stat_data.latency2 = latency2;
stat_data.f1f0 = f1f0;
stat_data.f2f1f0 = f2f1f0;
stat_data.f2f1 = f2f1;
stat_data.cid = cid;
stat_data.tag = tag;
stat_data.exited = exited;
stat_data.ave_IGR2 = ave_IGR2;
stat_data.ave_IGR1 = ave_IGR1;
stat_data.ave_latency = ave_latency./1000;
stat_data.fast_phy_neon = fast_phy_neon;
stat_data.Icell = Icell_ind;
stat_data.shifted = shifted_ind;
stat_data.log_phase_diff = log(abs(phase_diff));
stat_data.phase_diff = phase_diff;
stat_data.twopi_phase_diff = twopi_phase_diff;
stat_data.h_simplicity = h_simplicity;
stat_data.norm_rel_amp_f1 = norm_rel_amp_f1;
stat_data.surround_suppression = S_S;
stat_data.TPlatency = TPlatency;
stat_data.Depth = Depths;
stat_data.PTratio = PTratio;
stat_data.F1_dominant = logical(F1_dominant);
stat_data.preferred_ang = preferred_ang;
stat_data.OSI = OSI;
stat_data.DSI = DSI;
stat_data.RF_size = RF_size;
stat_data.RF_loc = RF_loc;
stat_data.RF_label = RF_label;
stat_data.RF_size_area = RF_size_area;
stat_data.Cell_area = Cell_area;
stat_data.first_comp = first_comp;
stat_data.zero_comp = zero_comp;
save([data_folder,'/neon_stat_data.mat'],'stat_data')
%%
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