Analyzing particles with masking specific areas (not to be analyzed)

Dear All,

I’m a beginner in ImageJ. I have a question about analyzing particles with masking specific areas.
I attached 2 example images which are acquired from different layers (‘superficial’ and ‘deep’) at the same tissue location.
Using ‘deep’ layer image, I want to analyze the multiple ROIs of rectangular shape(yellow ROIs). As you can see, there are dark shadow lines(large superficial blood vessels) projected from the superficial layer. So I want to exclude the shadow areas from analyzing.
How to apply binary mask from ‘superficial’ image to ‘deep’ layer and analyze the ROIs in deep layer with excluding the masked areas from analyzing?

Thanks
Kind regards,
Yongsok

Sorry for the delay in response @yongsok.ji … I think there is some missing information in order to get you some help. For example, when you say…

What exactly do you want to analyze? Too - when talking about ‘superficial layers’ and ‘deep layers’… keep in mind that we don’t necessarily know to which images you are referring… We don’t know this biology.

Perhaps what you want to do is use one layer to delineate those vessels and then exclude those regions from the analysis in the other layer? Is that correct?