I find CellProfiler very helpful in quantifying the intensity of two cytoplasmic proteins, and would like to analyze their correlation with another nuclear factor, yet this requires the use of four color analysis.
To identify the nucleus I used DAPI (blue) and the other two proteins are stained in green and red, the fourth protein was stained with Cy5 and I have pseudo-colored it in white. My question is how can preform four color analysis using CellProfiler? when I created four image files (one for each color) I was not able to use all four and only red, blue and green.
Thanks a lot,