Count amount of detected ROIs inside a ROI

[harkonsen]

Hi all,

as the headline already indicates do I want to measure how much ROIs there are within/surrounded by a larger ROI. To be more precise I have pictures of cells and I wanna know how much stained areas of interest there are within my cell. I detect these areas with particle analyzer and have them as ROIs and as I have plenty of cells within a picture I have to somehow ROI my cell and then know how much of these detected particles/ROIs there are.

[harkonsen]

ok here i found something that almost does the trick:

http://microscopy.duke.edu/HOWTO/countfoci.html

but as i have plenty of pictures I would need a macro, something like this:

--> at first I ROI my cells and afterwards I use the find maxima function within the same channel, but It doesnt redirect to the find maxima output picture:

run("Find Maxima...", "noise=50 output=[Single Points]");
selectWindow("ImageX.lsm");
roiManager("Show All");
roiManager("Measure");

please help me

[harkonsen]

I am overwhelmed by the help of this nice community