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mainSomitoid_Mesp2Uncx.m
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mainSomitoid_Mesp2Uncx.m
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%% calculate ROI1 - set 1
setnames = {'sub14'};
for n=1:numel(setnames)
paths.masterFolder = [pwd '/data/somitoid/mesp2uncx/'];
paths.inFolder = [paths.masterFolder 'raw/'];
paths.basename = ['Mesp2_24pt5hr start_20min interval_2020_11_20__15_34_56_' setnames{n}];
paths.savename = strrep(paths.basename,'Mesp2','ROI');
paths.objFolder = [paths.masterFolder 'objects/'];
img = imread([paths.inFolder paths.basename '.tif'],1);
img1 = imgaussfilt(img,5);
bw=imbinarize(img1);
bw2= imclose(bw,strel('disk',10));
bw3 = bwmorph(imfill(bw2,'holes'),'majority');
bw4 = bwareaopen(bw3,1000);
erosionROI = 50; %in px
warning('Erosion is in px');
roi = imerode(bw4,strel('disk',erosionROI));
saveOptions.compress = 'lzw';
saveOptions.overwrite = true;
saveastiff(uint8(roi),[paths.inFolder strrep(paths.savename,'T1ForROI','14Test') '.tif'],saveOptions); %for compatibility
imshowpair(img,roi)
end
%% merge mesp2 and uncx
setnames = {'sub14'};
for n=1:numel(setnames)
paths=[];
paths.masterFolder = [pwd '/data/somitoid/mesp2uncx/'];
paths.inFolder = [paths.masterFolder 'raw/'];
stdir=dir([paths.inFolder 'Uncx*' setnames{n} '*']);
paths.basename1 = strrep(stdir(1).name,'.tif','');
paths.basename2 = strrep(paths.basename1,'Uncx','Mesp2');
paths.basenameMerged = strrep(paths.basename1,'Uncx','Merged');
paths.basenameROI= strrep(paths.basename1,'Uncx','ROI');
paths.objFolder = [paths.masterFolder 'objects/'];
s1 = loadtiff([paths.inFolder paths.basename1 '.tif']);
s2 = loadtiff([paths.inFolder paths.basename2 '.tif']);
roi = loadtiff([paths.inFolder paths.basenameROI '.tif'])>0;
s1(~roi)=NaN;
s2(~roi)=NaN;
tot1 = nansum(nansum(s1,1),2)./nansum(nansum(roi,2),1);
tot2 = nansum(nansum(s2,1),2)./nansum(nansum(roi,2),1);
%plot(squeeze(tot1)); hold on; plot(squeeze(tot2));
m1 = repmat(tot1,[size(s1,1) size(s1,2)]);
m2 = repmat(tot2,[size(s2,1) size(s2,2)]);
s3 = ((double(s1)./m1-double(s2)./m2).*(m1+m2)./2)+(2^16-1)./2;
saveOptions.compress = 'lzw';
saveOptions.overwrite = true;
saveastiff(uint16(s3),[paths.inFolder paths.basenameMerged '.tif'],saveOptions);
end
%% process all sets
setnames = {'sub14'};
for n=1:numel(setnames)
% create somitoid
paths=[];
paths.masterFolder = 'data/somitoid/mesp2uncx/';
paths.inFolder = [paths.masterFolder 'raw/'];
paths.basename = ['Mesp2_24pt5hr start_20min interval_2020_11_20__15_34_56_' setnames{n}];
paths.ROIname = strrep(paths.basename,'Mesp2','ROI');
paths.resFolder = [paths.masterFolder 'plotSpCorr/'];
paths.objFolder = [paths.masterFolder 'objects/'];
mkdir(paths.resFolder);
mkdir([paths.resFolder '/png/']);
mkdir(paths.objFolder);
[myPSM0]=createSomitoid(paths);
% process somitoid
opts=[];
opts.tStep= 1;
opts.tStart = round((24.5-myPSM0.t0)./myPSM0.dt)+1;
opts.tEnd = round(90./myPSM0.dt-myPSM0.t0./myPSM0.dt)+1;
opts.tEnd = myPSM0.tMax;
opts.tStepPrint = round(6/myPSM0.dt); %hours/dt
opts.tStepPrintFine = round(3/myPSM0.dt); %hours/dt
opts.tEndFine = round((50-myPSM0.t0)./myPSM0.dt)+1;
opts.tPrint = [opts.tStart:opts.tStepPrintFine:opts.tEndFine opts.tEndFine:opts.tStepPrint:opts.tEnd];
opts.barPlotLim = [20 100];
opts.resFactor = 5.5/myPSM0.dx;
opts.dStep = 15; % 15 default in um
opts.xLimUm = [0 400];
opts.xMaxAutocorrUm = 200;
opts.gaussFiltParams = [25 50 280 280]; %in um, first two are smoothening, the other two for bk removal
%opts.gaussFiltParams = [2 4 280 280]; %in um, first two are smoothening, the other two for bk removal
opts.noGca = 1;
opts.sizeMultipliers = [1.2 1.1];
opts.verbose = true;
opts.toPrint = true;
opts.fractionMinMin = 0.95;
opts.valueMinMin = -0.02;
opts.valueMinStd = 2;
%
paths.basename = strrep(paths.ROIname,'ROI','Merged');
opts.label = 'Merged';
opts.labelPrint = 'Mesp2 and Uncx';
[myPSM,figs]=spCorrSomitoid(myPSM0,paths,opts);
save([paths.objFolder paths.basename],'myPSM');
myPSM_merged{n} = myPSM;
%
paths.basename = strrep(paths.ROIname,'ROI','Mesp2');
opts.label = 'Mesp2';
opts.labelPrint = 'Mesp2';
[myPSM,figs]=spCorrSomitoid(myPSM0,paths,opts);
save([paths.objFolder paths.basename],'myPSM');
myPSM_mesp2{n} = myPSM;
paths.basename = strrep(paths.ROIname,'ROI','Uncx');
opts.label = 'Uncx';
opts.labelPrint = 'Uncx';
[myPSM,figs]=spCorrSomitoid(myPSM0,paths,opts);
save([paths.objFolder paths.basename],'myPSM');
myPSM_uncx_{n} = myPSM;
end
%% recalculate and plot correlations with tBin
setnames = {'sub14'};
labels = {'Merged','Mesp2','Uncx'};
labelsPrint = {'Mesp2 and Uncx','Mesp2','Uncx'};
colors = lines(10);
colorsPrint = [0.5 0.5 0.5 ;colors([4 5],:)];
paths=[];
paths.masterFolder = 'data/somitoid/mesp2uncx/';
paths.objFolder = [paths.masterFolder 'objects/'];
paths.resFolder = [paths.masterFolder 'sprCorrPlotTbin/'];
mkdir(paths.resFolder);
mkdir([paths.resFolder '/png/']);
mkdir(paths.objFolder);
opts=[];
opts.barPlotLim = [20 100];
opts.posyPlotLim = [80 160];
opts.tBinH = 3;
opts.fractionMinMin = 0.95;
opts.valueMinMin = -0.02;
opts.valueMinStd = 2.5;
opts.verbose = true;
opts.toPrint = true;
opts.xLimUm = [0 400];
opts.xMaxAutocorrUm = 200;
for n=1:numel(setnames)
% process somitoids
for i = 1:numel(labels)
stdir=dir([paths.objFolder labels{i} '*' setnames{n} '.mat']);
load([paths.objFolder stdir(1).name]);
opts.tStep = 1;
opts.tStart = round((24.5-myPSM.t0)./myPSM.dt)+1; %70 - in frames
opts.tEnd = round(90./myPSM.dt-myPSM.t0./myPSM.dt)+1; %to be checked
opts.tStepPrint = round(6/myPSM.dt); %hours/dt
opts.tStepPrintFine = round(3/myPSM.dt); %hours/dt
opts.tEndFine = round((50-myPSM.t0)./myPSM.dt)+1;
opts.tPrint = [opts.tStart:opts.tStepPrintFine:opts.tEndFine];
opts.tPrint = [opts.tPrint opts.tPrint(end)+opts.tStepPrint:opts.tStepPrint:opts.tEnd];
myPSM.label = labels{i};
myPSM.labelPrint = labelsPrint{i};
myPSM.basename = stdir(1).name;
myPSM=spCorrTBinRecal(myPSM,paths,opts);
myPSM.colorPrint = colorsPrint(i,:);
save([paths.objFolder myPSM.basename],'myPSM');
myPSM_merged{n} = myPSM;
end
end