Fluorescence intensity of each pixel of the image


Hi all,

is there any possibility to quantify the fluorescence intensity of each pixel of an image?
It became important because I want to verify if there is a consistent background in a series of images I am currently analyzing.

Thanks in advance for your help,



Hi Dominik,

There are a few ways you can quantify the fluorescence intensity, two manual and one automatic:

(1) If you want a quick view of the intensity values associated with an image, you can open the image in CellProfiler, use CellProfiler Image Tools (under the menu bar) and select ShowOrHidePixelData. You’ll then see your mouse turn into a cross-hair and an info box appear at the bottom left. The image pixel values can be seen in the info box by mousing over the image.

(2) Another way is to look at the image histogram. Clicking on an image brings up the Image Tool box, from which you can select “Show intensity histogram.” This graphically shows the frequency with which pixel intensities occur in the image.

(3) Lastly, you can use the Measurement modules to automate quantification. MeasureImageIntensity will give you the total and mean intensity over the entire image. If you’ve managed to isolate the background as an object using the Identify modules, you can use MeasureObjectIntensity to quantify the background intensity while ignoring the foreground.

Hope this helps!