Nothing
library(bioimagetools)
setwd("/home/schmid/projects/marion/C2C12Xpaint")
files<-sample(list.files("green"))
for (file in files)
{
try({
print(file)
mask<-readTIF(paste("dapimask/",file,sep=""))
gb<-readTIF(paste("rgb/",file,sep=""))
blau<-gb[,,2,]
green<-gb[,,1,]
prot<-readTIF(paste("green/",file,sep=""))
#pm<-median(prot)
#prot[mask==0]<-pm
# prot<-prot*2^16
# storage.mode(prot)<-"integer"
brush<-makeBrush(25,shape="gaussian",sigma=2)
prot.smooth<-filterImage2d(prot,brush)
dens<-density(prot[mask==1&prot>.1],from=.1,to=.5)
dens.smooth<-density(prot.smooth[mask==1&prot.smooth>.1],from=.1,to=.5)
thresh1 <- dens$x[dens$y<dens.smooth$y]
thresh1 <- min(thresh1[thresh1>.1])
thresh2 <- dens$x[dens$y>dens.smooth$y]
thresh2 <- min(thresh2[thresh2>.2])
prot.mask<-ifelse(prot.smooth>.5*(thresh1+thresh2),1,0)
prot.objects<-bwlabel3d(prot.mask)
prot.moments<-cmoments3d(prot.objects,prot)
w<-sort(prot.moments[,5],decreasing=TRUE)
w<-which(prot.moments[,5]>=w[4])
prot.mask<-array(0,dim(prot.objects))
for (i in w)
prot.mask[prot.objects==i]<-1
#rgb<-array(NA,c(dim(prot)[1:2],3,dim(prot)[3]))
#rgb[,,1,]<-prot.mask
#rgb[,,2,]<-green
#rgb[,,3,]<-blau
#writeImage(rgb,file=paste0("x_mask/",file),bits.per.sample=8L)
writeTIF(prot.mask,file=paste0("x_mask/",file),bps=8L)
})
}
if(0)
{
nr.xi<-2
if(length(grep("mES",file))==0)nr.xi<-2
if(dim(prot5)[1]==1)nr.xi<-1
which<-rev(order(prot5[,5]))[1:nr.xi]
xi<-prot5[which,2:4]
xi.mask<-list()
for (i in 1:nr.xi)
xi.mask[[i]]<-(prot4==which[i])
# blue<-readImage(paste("rgb/",substr(file,0,18),"blue.tif",sep=""))
# test<-rgbImage(blue=blue,green=prot,red=xi.mask[[1]])
# writeImage(test,file=paste("xistbereich/1_",file,sep=""))
# if(nr.xi==2)
# {
# test<-rgbImage(blue=blue,green=prot,red=xi.mask[[2]])
# writeImage(test,file=paste("test_",file,sep=""))
# }
save(xi.mask,file=paste("xist/",substr(file,0,17),".Rdata",sep=""))
}
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