Re: Determining Mean Fluorescence Intensity

Posted by Liqun Zhang on Aug 09, 2006; 9:51pm
URL: http://imagej.273.s1.nabble.com/Determining-Mean-Fluorescence-Intensity-tp3684719p3684721.html

I have a similar question. How is the "auto" threshold determined? i.e.,
What is the algorithm behind it?
I'm no programmer, and do not understand the code.
Could some one enlighten me and/or point me to the right documents? Many
thanks.
Liqun

Lena wrote:

>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
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