Re: Determining Mean Fluorescence Intensity

Posted by Volker Baecker on Aug 10, 2006; 8:49am
URL: http://imagej.273.s1.nabble.com/Determining-Mean-Fluorescence-Intensity-tp3684719p3684722.html

Look here for information about the ImageJ auto-threshold:
http://imagejdocu.tudor.lu/imagej-documenation-wiki/faq/what-is-the-algorithm-used-to-threshold-images
Cheers,
Volker

Liqun Zhang a écrit :

> 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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