[BioC] computing segment areas on an image after thresholding

Ravi [guest] guest at bioconductor.org
Fri Aug 3 19:55:48 CEST 2012

I would like to develop a method for meassuring the percent area of a certain phase in an image. I have looked at packages EBImage and CRImage. But I am not able to make much headway. My code looks like this :
img = readImage(system.file("images", "nuclei.tif", package="EBImage"))[,,1]
#x = thresh(img, 10, 10, 0.05)
#x = opening(img, makeBrush(5, shape=’disc’))
#x = bwlabel(x)
fts = computeFeatures.shape(i1[,,1])

computeFeatures.shape seems to require a 2D array. But even the binary image has a dim 0f 510*510*4.
I would like to have help with the following questions :
1. From any general image, how do I create a binary image after using different thresholding criteria (to start with, the otsu method).
2. Sum all the segment areas corresponding to the phase of interest and then get the percent area.
3. I would like to have some help in interpreting the results of the last command (computeFeatures.shape) when I vary the third dimension from 1 to 4. The s.area results are different. What does this mean? How does one get a binary image without this variation?

 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)

[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 survival_2.36-14  
 [7] 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_7.3-19     stats4_2.15.1  
[8] tools_2.15.1  

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