How to measure the light intensity in different ROIs

Hello People,

I am new to ImageJ / Fiji and no native English speaker so my humble apologies in advance.
I am looking for a solution to the following task: I want the values of the pixels in different ROIs in the same photo, preferably in a list or so, to quantify the light intensity in the respective ROI in the picture.
The idea is to be able to quantify the amount of light transmitting a certain material via color photographies. To do so I took photos in a raw format and exported them to a composite 16-bit TIF, with respective values for the RGB channels to analyze it.
What I am looking for specifically is a way to extract the pixel values for each channel and the channels combined to be able to estimate the light intensity in certain ROIs to be able to further process the data.
As I am a new user I unfortunately can not upload an image, also they are rather large (about 140mb), so if anybody has a suggestion how to further illustrate it with a sample picture please let me know.

Thank you all in advance!

you can use the roi-manager (Analyze>Tools>ROI Manager) to store a list of ROIs. Open the tool, make a ROI with one of the selection tools from ImageJ (Rectangle, Freehand…) and add it to the ROI-manager.
If your image is a Hyperstack with 3 channels you can now use the More>Multi Measure command from the ROI-manager. You might need to select the properties you want to measure using Analyze>Set Measurements before. Make sure Integrated Density or Mean gray value are selected.
At this point the only thing missing for this image is the combined value of the three channels. On the Results table select Edit>Apply Macro and paste the following code (or something similar depending on what measure and what kind of combination you want to use) into the window that opens:

IntDenRGB = (IntDen1 + IntDen2 + IntDen3) / 3

This will add a column with the combined values to the results table.

You could automatize the whole procedure with a macro.

Of course you have to make sure that the values you measure really represent the light transmitting the material which might not be trivial.

Good luck,


thank You for Your reply.
Using the code line I get the following error:
Undefined variable in line
IntDenRGB = ( IntDen1 + IntDen2 + “<“IntDen3”>” ) / 3
Line number is on clipboard.

the names in the code that you run from the results table Edit>Apply Macro must correspond to the names of the columns in the results-table from which you run it. If you had an image with 3 channels and you did the More>Multi Measure you should have the 3 columns IntDen1, IntDen2 and IntDen3 in the table. Please check.
Best regards,