Hs.dirPath = pwd;
[Hs.dataFiles,Hs.dataNums] = getDataFiles(Hs.dirPath);
[Hs.foundChannels,Hs.fileNums,Hs.imgExts] = getImageFiles(Hs.dirPath);
for i = 1:length(Hs.fileNums)
Hs.fileNum = Hs.fileNums(i);
fileName = ['dapi' sprintf('%03d',Hs.fileNum) '.tif'];
Hs.DI = readmm(fileName);
Hs.DI = Hs.DI.imagedata;
Hs.DI = scale(max(Hs.DI(:,:,round(linspace(10,size(Hs.DI,10),50))),[],3));
binDapi = Hs.DI>adaptthresh(Hs.DI);
masktmp = imclearborder(binDapi | ~Hs.DI);
masktmp = bwareaopen(masktmp,50);
if any(masktmp(:))
binDapi = masktmp;
end
L = bwlabel(binDapi);
numObjects = max(L,[],1:2);
Hs.currObjs = [];
Hs.allMasks = [];
for j = 1:numObjects
fnumStr = sprintf('%03d',Hs.fileNum);
objMask = L == j;
newObj = improc2.buildImageObject(objMask, fnumStr, Hs.dirPath);
Hs.currObjs = [Hs.currObjs, newObj];
Hs.allMasks = cat(3,Hs.allMasks,objMask);
end
objects = Hs.currObjs;
save(sprintf('%s%sdata%03d.mat',Hs.dirPath,filesep,Hs.fileNum),'objects');
[Hs.dataFiles,Hs.dataNums] = getDataFiles(Hs.dirPath);
clear objects;
Hs.currObjs = [];
end
