Hi, I am now able to calculate the percent area of a certain phase on an image(thanks to the excellent help that I have received from this forum). My follow-up question is as follows : Depending on the threshold level chosen to create a binary image, the percent area calculated will vary. I would like to have a means of visualizing the uncertain regions represented by a threshold band level on the original image. If we start with the following code : library(CRImage) img = readImage(system.file("images", "nuclei.tif", package="EBImage"))[,,1] display(img) t1=calculateOtsu(as.vector(img));t1c<-t1*255 tdiff<-30 t2c<-t1c+tdiff; t2=t2c/255 # A second threshold level timg<-table(img) names(timg)<-1:255 plot(timg) # open to suggestions for better coding! abline(v=c(t1c,t2c),col="red") imgB=createBinaryImage(img,threshold=t1) imgB=!imgB #flip foreground to background imgS=bwlabel(imgB) fShape=computeFeatures.shape(imgS) percentArea=sum(fShape[,'s.area'])/length(img)*100 percentArea # Attempt to visualise the area represented by a threshold band i,e, (t2-t1) img2<-img crop1<-which(img2<t1) crop2<-which(img2="">t2) crop<-c(crop1,crop2) img2[crop]<-1 display(img2) # does not appear to be correct # the area seems to much greater than the 0.5% # obtained from the results of thresholding with t1 & t2 I don't think that img2 gives what I am hoping to get. As I mentioned previously, my intention is to identify the regions in img with intensity levels between t1 and t2 (the threshold band level represented by the red lines in the image histogram figure). I am interested in the following : 1. To color the uncertain regions in img2 with let???s say red colour and even have the choice of making it transparent. To then superpose img2 on top of the original image. 2. Maybe the reverse process is better. To make the original figure transparent and superpose it on img2. I am perhaps asking for too much. But I would appreciate any tip that I can get. Thanks, Ravi Sutradhara -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 LC_MONETARY=Swedish_Sweden.1252 [4] LC_NUMERIC=C LC_TIME=Swedish_Sweden.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] CRImage_1.6.0 aCGH_1.34.0 multtest_2.12.0 Biobase_2.16.0 BiocGenerics_0.2.0 [6] survival_2.36-14 cluster_1.14.2 DNAcopy_1.30.0 EBImage_3.12.0 abind_1.4-0 loaded via a namespace (and not attached): [1] class_7.3-4 codetools_0.2-8 e1071_1.6 foreach_1.4.0 iterators_1.0.6 MASS_7.3-20 stats4_2.15.1 [8] tools_2.15.1 -- Sent via the guest posting facility at bioconductor.org.

On 06.08.2012 16:26, Ravi [guest] wrote: > Hi, > I am now able to calculate the percent area of a certain phase on an > image(thanks to the excellent help that I have received from this > forum). My follow-up question is as follows : > Depending on the threshold level chosen to create a binary image, the > percent area calculated will vary. I would like to have a means of > visualizing the uncertain regions represented by a threshold band > level on the original image. If we start with the following code : > library(CRImage) > img = readImage(system.file("images", "nuclei.tif", > package="EBImage"))[,,1] > display(img) > t1=calculateOtsu(as.vector(img));t1c<-t1*255 > tdiff<-30 > t2c<-t1c+tdiff; t2=t2c/255 # A second threshold level > timg<-table(img) > names(timg)<-1:255 > plot(timg) # open to suggestions for better coding! hist(img*255) Gives you (almost) the same plot without the intermediate table step. > abline(v=c(t1c,t2c),col="red") > > imgB=createBinaryImage(img,threshold=t1) > imgB=!imgB #flip foreground to background > imgS=bwlabel(imgB) > fShape=computeFeatures.shape(imgS) > percentArea=sum(fShape[,'s.area'])/length(img)*100 > percentArea > # Attempt to visualise the area represented by a threshold band i,e, > (t2-t1) > img2<-img > crop1<-which(img2<t1)> crop2<-which(img2>t2) > crop<-c(crop1,crop2) > img2[crop]<-1 > display(img2) > # does not appear to be correct > # the area seems to much greater than the 0.5% > # obtained from the results of thresholding with t1 & t2 I'm not sure where you get 0.5% from? I get ~2.5% > (length(which(img >= t1 & img <= t2))/length(img))*100 [1] 2.614379 Very hard for me to judge by eye, but the displayed image looks about right and I can't see an error in the code/logic. > I don't think that img2 gives what I am hoping to get. As I mentioned > previously, my intention is to identify the regions in img with > intensity levels between t1 and t2 (the threshold band level > represented by the red lines in the image histogram figure). > I am interested in the following : > 1. To color the uncertain regions in img2 with let???s say red colour > and even have the choice of making it transparent. To then superpose > img2 on top of the original image. > 2. Maybe the reverse process is better. To make the original figure > transparent and superpose it on img2. Lots of different ways to do this, but does this get you started? img3 = rgbImage((!img2)+img,img,img) display(img3) > I am perhaps asking for too much. But I would appreciate any tip that > I can get. > Thanks, > Ravi Sutradhara > > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 > LC_MONETARY=Swedish_Sweden.1252 > [4] LC_NUMERIC=C LC_TIME=Swedish_Sweden.1252 > > attached base packages: > [1] splines stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] CRImage_1.6.0 aCGH_1.34.0 multtest_2.12.0 > Biobase_2.16.0 BiocGenerics_0.2.0 > [6] survival_2.36-14 cluster_1.14.2 DNAcopy_1.30.0 > EBImage_3.12.0 abind_1.4-0 > > loaded via a namespace (and not attached): > [1] class_7.3-4 codetools_0.2-8 e1071_1.6 foreach_1.4.0 > iterators_1.0.6 MASS_7.3-20 stats4_2.15.1 > [8] tools_2.15.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Alex Gutteridge