I’m trying to calculate the signal to background ratio of my cell staining in image J. Is there an easy way to do that? I can threshold cells and limit measurements to threshold to get the average intensity of my stained cells, but how do I get the average intensity the non thresholded regions only. I do not see an option for that. I know I can draw regions around the non-thresholded areas to get those measurements but that seems biased and cumbersome.
I can think of various ways how you could measure your background depending on how you want to define your background:
You can get a measurement of the average intensity of all the image area that is not part of one of your ROIs by selecting all ROIs and then combining them (ROI manager → More → OR(combine)). This creates a selection of all you ROIs. You can then invert the selection (Edit → Selection → Make Inverse) and measure it (Analyze → Measure). This would give you a global background measure.
Alternatively, you could select ROIs individually and use the ‘Make Band’ option (Edit → Selection → Make Band) to create a selection of a defined width around your ROI and measure this. This will give you a more local background around each ROI.
Hope this helps,
This is great Volko, I believe a version of this is working. Thanks for the idea!