Calculation for FRET


I would like to know if with cell profiler I can do a pipeline similar to an Image J macros, this is part of the macro that I want to test in cell profiler

img = File.nameWithoutExtension();
run(“Subtract Background…”, “rolling=300 stack”);
run(“StackReg”, “transformation=Translation”);
run(“Median…”, “radius=1.3 stack”);
run(“Stack to Images”);
run(“Duplicate…”, “title=mask”);
setAutoThreshold(“Default dark”);
waitForUser("Imagen “+n+” de "+length,“Apply Threshold y click OK”);
run(“Divide…”, “value=255”);
saveAs(“Tiff”, path + “Imaging/mask 000” + i);

           imageCalculator("Divide create 32-bit","Ch3","Ch2");

           imageCalculator("Multiply create","Result of Ch3","mask 000"+i+".tif");
           selectWindow("Result of Result of Ch3");
           saveAs("Tiff", path + "Imaging/fret map " + i);

I want to do this for a whole folder; my problem is that every image has a different name (e.g., Control 1, Control, 2, Treatment 1, Treatment 2) and I cannot make this macro generic to identify any image in one folder and perform the calculations. So I want to know if Cell profiler can do it.

Any advice, I will appreciate

Thanks in advance.


CellProfiler could do very likely do all of that, though Align (the equivalent of the StackReg step ) can be kind of slow. Just the ImageMath and ApplyThreshold modules would take care of almost all of that.

Another option (that I’ve personally used successfully on folders of images with different names) would be instead of using macros in ImageJ to use scripts. Here’s a link to ImageJ tutorials in a bunch of scripting languages; I’m partial to Python, but whatever works for you.