Hi there,
I was wondering if anyone can tell me how to quantify fluorescence
intensity with image J. I don't need to analyze single cells, I just want to measure the fluorescent intensity of an image (or selected area of an image) and compare with others taken under same conditions.
According to the protocol I know that I have to do the following:

1. Convert the color picture to 8it-b black and white scale.
2. Subtract the background fluorescence equivalently for all images by setting the threshold to 50% maximum intensity.
3. To quantify the mean fluorescence
I will appreciate if someone can post a tutorial with screen-shots regarding my question.

Thank you in advance for your help

There are lots of online tutorials and protocols for imagej, as it's open source. Do some googling, you might find what you need. If you still have a question after that, you'd probably have better luck posting on one of the imagej forums, than on here.

One tip: people are more likely to help you if you have a specific question, and can show that you've tried to find out the answer on your own first.

ImageJ is no big deal. Your question is confusing. What is fluroescent intensity. Points 1,2,3 do not make much sense..

Hi Polikarp,

I use Fiji for image J.

Select your region of interest and chose histogram from under the analyze menu.
The histogram has a list option.
Copy the data into a spreadsheet and get the mean fluorescence that way.

The histogram is a good way to see similarity between images as similar tissue can have similar histogram shape even if the intensity max/min is different.
Remember that amount of fluorescence is not an absolute value unless the images you are comparing have been taken at exactly the same time under the same conditions.
The same method two days in a row on two slides from the same sample can give different intensity levels as the dyes will degrade with time or can be influenced by very subtle experimental conditions such as room temperature.

(Sorry not sure how to post screen shots)