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run_foci.m
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run_foci.m
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clear all
close all
SampleNum = '20';
FileName = ['Sequential/STORMCy5_00_' SampleNum];
load(['DriftParams' SampleNum '.mat']);
load('DeltaZ.mat');
load('tform.mat');
Color = ['r' 'g' 'b' 'c' 'm' 'y' 'k' 'r' 'g' 'b' 'c' 'm'];
[ImageStack, InfoFile] = ReadZStack(FileName,111,5);
ImageMean = mean(ImageStack,3);
% Here warp the Cy5 image into the Cy3 channel.
ImageMean_trans = imtransform(ImageMean, tform, 'XData', [1 256], 'Ydata', [1 256], 'fill', min(min(ImageMean)));
figure(100)
imagesc(ImageMean_trans)
colormap gray
axis equal
% imwrite(uint16(ImageMean),strcat('Fig100', '.tiff'),'tiff');
NewROI = questdlg('Do you want to select new ROI?'); %ask question
if(strcmp(NewROI, 'Yes'))
selectROI
save(['roiList' SampleNum '.mat'],'roiList')
else
load(['roiList' SampleNum '.mat']);
end
roiListBig = roiList;
for ii = 1:length(roiListBig)
figure(200+ii)
imagesc(ImageMean_trans)
colormap gray
axis equal
xlim([roiListBig(ii).rect(1) roiListBig(ii).rect(1)+roiListBig(ii).rect(3)]);
ylim([roiListBig(ii).rect(2) roiListBig(ii).rect(2)+roiListBig(ii).rect(4)]);
hold on
if(~strcmp(NewROI, 'Yes'))
load(['result' SampleNum '_' num2str(ii) '.mat']);
else
Real = ones(27,1);
end
Xfit = zeros(27,1);
Yfit = zeros(27,1);
Zfit = zeros(27,1);
for i = 1:14
if i<10
FileName = ['Sequential/STORMCy5_0' num2str(i) '_' SampleNum];
else
FileName = ['Sequential/STORMCy5_' num2str(i) '_' SampleNum];
end
[ImageStack, InfoFile] = ReadZStack(FileName,111,5);
% Here warp the Cy5 image into the Cy3 channel.
for j = 1:size(ImageStack,3)
ImageStack(:,:,j) = imtransform(ImageStack(:,:,j), tform, 'XData', [1 256], 'Ydata', [1 256]);
end
roiNOW = roiListBig(ii);
roiNOW.rect = roiNOW.rect + [Xdrift(i) Ydrift(i) 0 0];
[Xfit(i), Yfit(i), Zfit(i)] = fitFoci(ImageStack, roiNOW, i, ii);
if Zfit(i)<1 || Zfit(i)>21
Real(i) = 0;
end
Xfit(i) = Xfit(i) - Xdrift(i);
Yfit(i) = Yfit(i) - Ydrift(i);
Zfit(i) = Zfit(i) - Zdrift(i);
end
for i = 15:27
j = i-14;
if j<10
FileName = ['Sequential/STORMCy3_0' num2str(j) '_' SampleNum];
else
FileName = ['Sequential/STORMCy3_' num2str(j) '_' SampleNum];
end
[ImageStack, InfoFile] = ReadZStack(FileName,111,5);
roiNOW = roiListBig(ii);
roiNOW.rect = roiNOW.rect + [Xdrift(j) Ydrift(j) 0 0];
[Xfit(i), Yfit(i), Zfit(i)] = fitFoci(ImageStack, roiNOW, i, ii);
if Zfit(i)<1 || Zfit(i)>21
Real(i) = 0;
end
Xfit(i) = Xfit(i) - Xdrift(j);
Yfit(i) = Yfit(i) - Ydrift(j);
Zfit(i) = Zfit(i) - Zdrift(j);
end
figure(200+ii)
plot(Xfit, Yfit, 'b-', 'LineWidth', 2);
plot(Xfit, Yfit, 'or', 'MarkerSize', 5, 'MarkerFaceColor', 'r');
for i = 1:27
text(Xfit(i), Yfit(i), num2str(i));
end
% now choose the dots that are not real and mark them.
for i = 1:27
if Xfit(i)<roiListBig(ii).rect(1) || Xfit(i)>roiListBig(ii).rect(1)+roiListBig(ii).rect(3) ||...
Yfit(i)<roiListBig(ii).rect(2) || Yfit(i)>roiListBig(ii).rect(2)+roiListBig(ii).rect(4)
Real(i) = 0;
end
end
for i = 1:27
if Real(i) == 0;
plot(Xfit(i), Yfit(i), 'og', 'MarkerSize', 5, 'MarkerFaceColor', 'g');
end
end
if(strcmp(NewROI, 'Yes'))
selectROI
for i = 1:length(roiList)
x = roiList(i).rect(1) + 0.5*roiList(i).rect(3);
y = roiList(i).rect(2) + 0.5*roiList(i).rect(4);
[C , I] = min(((Xfit-x).^2+(Yfit-y).^2).^0.5);
if C < 4
Real(I) = 0;
plot(Xfit(I), Yfit(I), 'og', 'MarkerSize', 5, 'MarkerFaceColor', 'g');
end
end
end
hold off
Xfit = Xfit*167/1000; %um
Yfit = Yfit*167/1000; %um
Yfit = 2*mean(Yfit)-Yfit;
Zfit(1:14) = Zfit(1:14)-DeltaZ;
Zfit = Zfit*0.2; %um
figure(300+ii)
plot3(Xfit, Yfit, Zfit,'LineWidth', 2);
hold on
for i = 1:27
if Real(i) == 0
scatter3(Xfit(i), Yfit(i), Zfit(i), 'og', 'MarkerFaceColor', 'g');
else
scatter3(Xfit(i), Yfit(i), Zfit(i), 'or', 'MarkerFaceColor', 'r');
end
end
hold off
xlabel('x');
ylabel('y');
zlabel('z');
if(strcmp(NewROI, 'Yes'))
save(['result' SampleNum '_' num2str(ii) '.mat'], 'Xfit', 'Yfit', 'Zfit', 'Real');
end
end