Quantifying GFP flourescence in .lif image files
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6.8 years ago
Tom A ▴ 110

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!

image-processing GFP microscopy • 2.0k views
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6.8 years ago
a.polo88 ▴ 110

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 programm perform the quantification of fluorescent intensity

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6.8 years ago

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.

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