Thank you very much for your help.
> When drawing ROIs, it's not necessary to threshold since the measurement
> will only be applied to region enclosed in the ROI.
>
> Thresholding is an alternative way to measure the pixel intensity value of
> your two different cell compartments that does not require ROIs. You can do
> the same thing as before by selecting "Limit to Threshold" in the
> Analyze->Set Measurements menu. This might actually be an easier way to do
> it if the intensity values between the two regions you're trying to
> investigate are well separated in intensity.
>
> John Oreopoulos
>
>
>
> On 2-Sep-09, at 8:11 PM, Giulia Falivelli wrote:
>
> Hi John,
>> Thanks for helping.
>> Sorry, should I set a threshold before calculate the mean fluorescence?
>>
>> Giulia
>>
>> On Wed, Sep 2, 2009 at 4:53 PM, John Oreopoulos <
>>
[hidden email]
>>
>>> wrote:
>>>
>>
>> Giulia,
>>>
>>> First, go to Analyze->Set Measurements and make sure "Mean Gray Value" is
>>> checked.
>>> Next, draw a region of interest on your image with the Rectangular
>>> Selection tool (or circular or freehand tools if your imaging situation
>>> demands it. To get the mean pixel intensity value within your region of
>>> interest, click Analyze->Measure, and the result will appear as a number
>>> in
>>> a results window.
>>>
>>> Move the region of interest to your other cell compartment where you want
>>> to measure the intensity value and do the same thing. Now you can take
>>> these
>>> two numbers and calculate a ratio by simple division.
>>>
>>> Beyond that, if you require automation/repetition or more
>>> complex/multiple
>>> regions of interest to be examined, you may want to try writing a macro
>>> that
>>> does this for you. Try looking through the long list of plugins available
>>> on
>>> the main ImageJ website and see if there is any plugin out there that
>>> already does this. None come to mind immediately, but perhaps there is a
>>> calcium imaging plugin that might do the trick for you. Hopefully someone
>>> else here on the server can suggest one.
>>>
>>> John Oreopoulos
>>>
>>>
>>>
>>> On 2-Sep-09, at 7:42 PM, Giulia Falivelli wrote:
>>>
>>> Hi All,
>>>
>>>>
>>>> I am new in Image J.
>>>> Does anybody know how to calculate the fluorescence ration between two
>>>> different cells compartement?
>>>> Or how to calculate the mean grey value of a specific ROI?
>>>> Thank you very much.
>>>>
>>>> Giulia
>>>>
>>>>
>>>