Measuring Fluorescence density of nuclei

Posted by Anoekvanleeuwen on Jun 10, 2014; 6:04pm
URL: http://imagej.273.s1.nabble.com/Measuring-Fluorescence-density-of-nuclei-tp5008116.html

Hi,

I have a question about measuring the amount of fluorescence with ImageJ.
I stained my nuclei with DAPI and I'm trying to measure the fluorescence density, and with this the amount of DNA.

First, I used a method to calculate the CTCF, where I drew a circle around the nucleus, and with CTRL + M I measured the area, mean grey value and Integrated Density. Unfortunately I found out that the size of the circle had influence on the CTCF, which in my opinion is not right.

Then I heard of a 'threshold' method. I tried to find more about this method, but the only thing I can find is that I should use the option Image > Adjust > Threshold. This sounds fine, but how do I know what setting I should use? And when I know the settings, should I just measure the whole picture? And after this, is the Integraded Density my outcome or should I use a calculation?

Another question, if I'm using the threshold method, how can I do this the easiest/fastest?
I have around 1500 pictures each containing one or two nuclei.

Thanks in advance!
Anoek