[BioC] computing segment areas on an image after thresholding
henrik.failmezger at googlemail.com
Fri Aug 3 21:28:48 CEST 2012
you can do that by:
img = readImage(system.file("images", "nuclei.tif", package="EBImage"))[,,1]
imgB=!imgB #flip foreground to background
you have to flip the background of the binary image, as bwlabel
considers pixel with value 0 as background, whereas createBinaryImage
converts dark objects on a light background to foreground.
You can get the area of the nuclei by: fShape[,"s.area"]
2012/8/3 Ravi [guest] <guest at bioconductor.org>:
> 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)
>  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
>  tools_2.15.1
> Sent via the guest posting facility at bioconductor.org.
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