Help getting started: color intensity in two ROI



Dear Colleagues,
Sorry for extremely naive questions, but I cannot figure out how to get started with a simple task in ImageJ2: compare the amount of red in two areas of an image (or of 2 images). Help and manuals are written with the expectation that the reader has a considerable knowledge in image analysis which I do not. I understand that the string in the bottom of ImageJ window displays coordinates and RGB intensities when I mouse over a RGB image. I also understand of course that I can save gray intensities by Analyze/Measure. However, 1) Set Measurements does not include the option to save RGB channels separately and 2) I cannot figure out how to limit measurements to a particular ROI. I understand that I can do Analyze/Tools/ROI Manager, where I can Add a ROI and then click Measure; I have a feeling that the saved measurements refer to the selected ROI, not the whole image, but I cannot figure out what these measurements are; I get something like 1 24748 59.142 44 85 - what are these numbers? They don’t look like either coordinates or intensities, either gray or separate channels.

My next question is about image analysis, not ImageJ2 interface. Ok, let’s say I figured out with your help how to save intensities in 3 channels for a particular ROI. Now, let’s say I want to demonstrate that one ROI has more red than the other; however they may also differ in overall brightness, so simply comparing R channel values in two ROIs won’t work. Is there a standard way to analyze this? Some sort of normalization like R/(R+B+G), weighted or not weighted?

Will be grateful for your advise!

RGB intensities in a ROI
Help: measure width, length and color of fruits

Nobody answer my previous question, perhaps because it was too wordy. So, very briefly: how do I record red green and blue intensities separately for a selected ROI?


You can transform an RGB Color image to an RGB stack using Image > Type > RGB Stack.

The Analyze > Measure command always respects the current selection. See also the ImageJ user guide.


thanks! guess I need to find out what are stacks and what to do next.


Yes, I recommend reading the user guide, and for your measurements also Color Image Processing on the wiki.

The ROI Manager offers a Multi Measure command that lets you measure a selection on each channel of a multi-channel image.


Hi, @

1 Did you find solutions ? I have a similar question.