Quantifying GFP flourescence in .lif image files

Question

[Tom A]

I have a ~ 100 .lif images that contain GFP fluorescent cluster "dots" and I need to basically quantify the intensity and spread in each picture file.

Does anyone have a suggestion on existing software or even an R package that I could use? Any and all suggestions are greatly appreciated.

Thanks in advance!

Answer 1

[a.polo88]

Hi,

I don't know if in R there is a program that is useful for your question, but there is a imageJ. If I remember well this program perform the quantification of fluorescent intensity

Answer 2

[Jean-Karim Heriche]

In R, you can try the Bioconductor EBImage package. As already suggested, ImageJ is a favorite amongst biologists but there are plenty of image processing toolkits out there that can do what you want. Here is a non-exhaustive list trying to cover different programming environments: Octave's image package, vigra (C++ with python bindings), python's scikit-image, perl's IPA module and PDL image-related modules.