Determining Mean Fluorescence Intensity

Posted by ev34 on Aug 09, 2006; 5:37pm
URL: http://imagej.273.s1.nabble.com/Determining-Mean-Fluorescence-Intensity-tp3684719.html

Hello,

I am new to ImageJ and trying to 1) how to figure out what the best
threshold value should be 2) how to determine the range of the particle size
that I need to set 3) how to calculate mean fluorescence intensity (how is
it related to mean pixel intensity, integrated density or mean particle
size? is it just the integrated particle size divided by the area?) I am
imaging intestinal fluorescence in C. elegans and need the program to pick
out the fluorescent granules. So far, it is picking up that and a lot of
other "junk" so that I have to manually scroll down the list to see which
integrated denisties have the highest values. My main concern is that I am
setting the threshold on "auto" run now without knowing if that's really the
best way to do it. Do all of my pictures have to have the same exposure time
if I want to compare them and keep the same threshold and particle size
settings? My other concern is that I am not sure what the lower limit of my
particle size should be.

Any help will be greatly appreciated. Thanks much!

Lena