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First_Extract_Column_Cells_PZ.m
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First_Extract_Column_Cells_PZ.m
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clear all
%
%
% dt_path_wt={ '../data/Nuclei_and_Cells_DT_S84_m3_wt/','../data/Nuclei_and_Cells_DT_S17_m2_wt/','../data/Nuclei_and_Cells_DT_S84_m4_wt/',...
% '../data/Nuclei_and_Cells_DT_S18_m6_wt/','../data/Nuclei_and_Cells_DT_S51_m2_wt/'};
% pt_path_wt = { '../data/Nuclei_and_Cells_PT_S84_m3_wt/','../data/Nuclei_and_Cells_PT_S17_m2_wt/','../data/Nuclei_and_Cells_PT_S84_m4_wt/',...
% '../data/Nuclei_and_Cells_PT_S18_m6_wt/','../data/Nuclei_and_Cells_PT_S51_m2_wt/'};
% dt_path_mut= {'../data/Nuclei_and_Cells_DT_S17_m1_mut/', '../data/Nuclei_and_Cells_DT_S18_m2_mut/' ,...
% '../data/Nuclei_and_Cells_DT_S84_m1_mut/', '../data/Nuclei_and_Cells_DT_S84_m5_mut/'};
% pt_path_mut = {'../data/Nuclei_and_Cells_PT_S17_m1_mut/', '../data/Nuclei_and_Cells_PT_S18_m2_mut/',...
% '../data/Nuclei_and_Cells_PT_S84_m1_mut/', '../data/Nuclei_and_Cells_PT_S84_m5_mut/', };
% du_path_wt={'../data/Nuclei_and_Cells_DU_S51_m2_wt/','../data/Nuclei_and_Cells_DU_S84_m2_wt/','../data/Nuclei_and_Cells_DU_S84_m3_wt/'};
dt_path_wt={ '../data/Nuclei_and_Cells_DT_S18_m6_wt/', '../data/Nuclei_and_Cells_DT_S17_m2_wt/',...
'../data/Nuclei_and_Cells_DT_S84_m3_wt/', '../data/Nuclei_and_Cells_DT_S51_m2_wt/',...
'../data/Nuclei_and_Cells_DT_S84_m4_wt/'};
pt_path_wt = { '../data/Nuclei_and_Cells_PT_S18_m6_wt/','../data/Nuclei_and_Cells_PT_S17_m2_wt/',...
'../data/Nuclei_and_Cells_PT_S84_m3_wt/','../data/Nuclei_and_Cells_PT_S51_m2_wt/',...
'../data/Nuclei_and_Cells_PT_S84_m4_wt/'};
dt_path_mut= {'../data/Nuclei_and_Cells_DT_S17_m1_mut/', '../data/Nuclei_and_Cells_DT_S18_m2_mut/' ,...
'../data/Nuclei_and_Cells_DT_S84_m1_mut/', '../data/Nuclei_and_Cells_DT_S84_m5_mut/'};
pt_path_mut = {'../data/Nuclei_and_Cells_PT_S17_m1_mut/', '../data/Nuclei_and_Cells_PT_S18_m2_mut/',...
'../data/Nuclei_and_Cells_PT_S84_m1_mut/', '../data/Nuclei_and_Cells_PT_S84_m5_mut/', };
du_path_wt={'../data/Nuclei_and_Cells_DU_S51_m2_wt/','../data/Nuclei_and_Cells_DU_S84_m2_wt/','../data/Nuclei_and_Cells_DU_S84_m3_wt/'};
allpath={dt_path_wt; pt_path_wt; dt_path_mut; pt_path_mut; du_path_wt};
%
%
% RZ{1}={[1:10],[16:25],[1:10],[1:14],[1:7]};
% RZ{2}={[1:10],[17:34],[1:12],[20:39],[16:30]};
% RZ{3}={[1:8],[15:22],[1:8],[17:25]};
% RZ{4}={[16:29],[1:14],[11:20],[1:10]};
% RZ{5}={[15:20],[1:6],[1:6]};
%
% PZ{1}={[11:16],[11:15],[11:16],[15:18],[8:14]};
% PZ{2}={[11:20],[12:16],[13:21],[10:19],[12:15]};
% PZ{3}={[9:14],[7:14],[9:14],[8:16]};
% PZ{4}={[8:15],[15:22],[7:10],[11:17]};
% PZ{5}={[10:14],[7:12],[7:12]};
%
% PHZ{1}={[17:19],[8:10],[17:19],[19:22],[15:17]};
% PHZ{2}={[21:24],[8:11],[22:25],[6:9],[9:11]};
% PHZ{3}={[15:17],[4:6],[15:17],[6:7]};
% PHZ{4}={[4:7],[23:26],[4:6],[18:19]};
% PHZ{5}={[7:9],[13:14],[13:15]};
%
% HZ{1}={[20:22],[1:7],[20:22],[23:30],[18:23]};
% HZ{2}={[25:30],[1:7],[26:31],[1:5],[1:8]};
% HZ{3}={[18:23],[1:3],[18:20],[1:5]};
% HZ{4}={[1:3],[27:29],[1:3],[20:24]};
% HZ{5}={[1:6],[15:21],[16:21]};
meanOfAllCelltemp=load('meanOfAllCell.dat');
count=1;
for gi=1:length(allpath)
for gj=1:length(allpath{gi})
GlobalCenter{gi}{gj}=meanOfAllCelltemp(count,1:3);
count=count+1;
end
end
for gi=1:length(allpath)
for gj=1:length(allpath{gi})
path=allpath{gi}{gj};
disp(path)
s=strsplit(path,'Nuclei_and_Cells_');
outputpath=strcat('MakeListColumnarStructurePrediction/',s{2});
if ~exist([outputpath],'dir')
mkdir([outputpath]);
end
if exist([outputpath,'centroid_and_surface_cells.mat'], 'file') == 0
alignment=load(['./../../',path,'Alignment_matrix.dat']);
vec=alignment(:,1:3);
[numbers,txt,raw] = xlsread(['./../../',path,'Tile_coordinates.xlsx']);
coordinates = zeros(size(txt,1)-3,5);
for i = 4:size(txt,1),
temp = char(txt(i,1));
res = strsplit(temp,'_POS');
coordinates(i-3,1) = str2num(char(res(2)));
coordinates(i-3,2:5) = numbers(i-3,:);
end
tile=coordinates(:,2:end);
clear alltileid
clear Repeat_surfaces
%clear Repeat_ellipsoid
clear Repeat_centroids
clear Repeat_pixels
%clear Repeat_triangulation
clear Repeat_volume
scount=1;
for position = coordinates(:,1)' % intersect(PZ{gi}{gj},coordinates(:,1)') %setdiff(coordinates(:,1)',RZ{gi}{gj})
load(strcat('./../../',path,'c_n_pos',num2str(position),' (Characteristics).mat'));
indtemp = find(G.inter.volume_ratio>1);
fi = find(coordinates(:,1) == position);
for i=1:length(indtemp)
j=indtemp(i);
%for j=1:size(C.coords,1)
value=G.cel.centroids(j,:)+ repmat([tile(fi,2), -tile(fi,1),tile(fi,3)],1,1);
Repeat_centroids(scount,:)=value*vec;
value=C.surfaces(j).vertices + repmat([tile(fi,2), -tile(fi,1),tile(fi,3)],1,1);
Repeat_surfaces{scount,1}=value*vec;
%Repeat_triangulation{scount,1}=C.surfaces(j).faces;
%value={G.cel.ellipsoid_center(j,:), G.cel.ellipsoid_radii(j,:), G.cel.ellipsoid_evecs{j}, G.cel.ellipsoid_v{j}};
%Repeat_ellipsoid{scount,1}=value;
Repeat_volume(scount,:)=G.cel.volume(j,:);
Repeat_pixels(scount,:) = calc_centroids(C.masks(j), C.origins(j,:));
alltileid(scount,:)=[fi,j];
scount=scount+1;
end
end
%[size(Repeat_centroids), size(Repeat_surfaces),]
[~,ia]=unique(Repeat_centroids,'rows');
centroid=Repeat_centroids(ia,:);
nuc=Repeat_surfaces(ia,:);
%fitellipsoid=Repeat_ellipsoid(ia,:);
unique_pixel=Repeat_pixels(ia,:);
unique_tileid=alltileid(ia,:);
%faces=Repeat_triangulation(ia,:);
celvolume= Repeat_volume(ia,:);
save([outputpath,'centroid_and_surface_cells.mat'],'nuc','centroid','celvolume','unique_pixel','unique_tileid','-v7.3');
else
load([outputpath,'centroid_and_surface_cells.mat']);
end
% meanCentroid=mean(centroid);
% [meanCentroid, GlobalCenter{gi}{gj}];
% [min(centroid(:,3)),max(centroid(:,3))]
bonetype=gi;
if (bonetype==3)|(bonetype==1)
tempCentroid=[centroid(:,1:2),-centroid(:,3)];
else
tempCentroid=[centroid(:,1:2),centroid(:,3)];
end
newcentroid=tempCentroid-GlobalCenter{gi}{gj};
PD_bins=linspace(min(newcentroid(:,3)),max(newcentroid(:,3)),11);
if exist([outputpath,'threshold_along_PD_axis.mat'], 'file') == 0
disp('calculate minimum negihbors distance');
[min_neigh_dist,clist,cel_normalizationFactor] = calculate_nuclei_density(newcentroid, [1, 1, 1], 2);
for i=1:10
index=find( (newcentroid(:,3)>PD_bins(i)) & (newcentroid(:,3)<=PD_bins(i+1)));
threshold(i)=mean(min_neigh_dist(index));
end
save([outputpath,'threshold_along_PD_axis.mat'],'threshold','-v7.3');
dlmwrite([outputpath,'threshold_along_PD_axis.dat'],threshold,'\n');
else
load([outputpath,'threshold_along_PD_axis.mat']);
end
%cellsInPZandPHZindex= find((newcentroid(:,3)>-100)&(newcentroid(:,3)<1000));
cellsInPZandPHZindex=find(newcentroid(:,3)>PD_bins(3));
RZtoHZrange=[min(newcentroid(:,3)),max(newcentroid(:,3))]
CellsInPZandPHZrange=[size(centroid,1),length(cellsInPZandPHZindex)]
%disp('I am here')
d=20;
fid=fopen([outputpath,'NeighboringCell_in_20_micron_cube.dat'],'w');
for i=1:length(cellsInPZandPHZindex)
main=centroid(cellsInPZandPHZindex(i),:);
normalized_main=newcentroid(cellsInPZandPHZindex(i),:);
for j=1:10
if( (normalized_main(3)>PD_bins(j)) & (normalized_main(3)<=PD_bins(j+1)))
cutoff=threshold(j);
end
end
%ankit(i,:)=[normalized_main(:,3),cutoff];
index=find(((main(1)-d)<=centroid(:,1)) & ((main(1)+d)>=centroid(:,1)) & ((main(2)-d)<=centroid(:,2)) & ((main(2)+d)>=centroid(:,2) ) & ((main(3)-d)<=centroid(:,3)) & ((main(3)+d)>=centroid(:,3) ) );
if length(index)>1
col=distance_between_neighbor_cell(centroid, index,cutoff);
for j=1:size(col,1)
fprintf(fid,'%d\t%d\t%0.4f\t%0.4f\n',col(j,1),col(j,2),col(j,3),col(j,4));
end
end
end
fclose(fid);
end
end
function [column]=distance_between_neighbor_cell(Cent,ind,cutoff)
C=Cent(ind,:);
n=size(C,1);
c2=1;
column=[];
for i=1:n
for j=i+1:n
ed=pdist(C([i,j],:));
zd=diff(C([i,j],3));
if ed<=cutoff
column(c2,:)=[ind(i),ind(j),ed,abs(zd)];
c2=c2+1;
end
end
end
end
function centroids = calc_centroids(masks, origins)
centroids = nan(length(masks),3);
for i = 1 : length(masks)
[x,y,z] = ind2sub(size(masks{i}), find(masks{i}));
centroids(i,:) = (mean([x,y,z],1) + double(origins(i,:) - 1));
end
end