[BioC] computing segment areas on an image after thresholding
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=âdiscâ))
#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)
 LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 LC_MONETARY=Swedish_Sweden.1252
 LC_NUMERIC=C LC_TIME=Swedish_Sweden.1252
attached base packages:
 splines stats graphics grDevices utils datasets methods base
other attached packages:
 CRImage_1.6.0 aCGH_1.34.0 multtest_2.12.0 Biobase_2.16.0 BiocGenerics_0.2.0 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):
 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
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