http://imagej.273.s1.nabble.com/Selecting-a-masked-overlayed-object-tp5004930p5004931.html
You have to use the ROI manager. On you thresholded image draw your
region of interest with the tool you need. Type "t" to have your region
> Hi,
> I am using Imagej to calculate the thresholded area and intensity of a
> selected area of staining (endplate receptor cluster and nerve terminal of
> neuromuscular junction) of two fluorescent channels. There are more than one
> staining areas (endplates) and I would like to calculate their intensity and
> area individually. I want to use the same area calculated by thresholding
> and transfer this area to the other channel.
>
> I can transfer the area surrounding the staining on one channel to the
> other. I do this by thresholding the channel. Then I use edit -> selection
> -> create selection.
>
> This creates a 'mask' of the area of the channel that is shown on both
> channels. However, I cannot use the polygon or freehand selection tools to
> isolate the area of staining that i would like to consider (individual
> endplate). When i threshold and measure it calculates the total intensity
> within all regions of staining (multiple endplates).
>
> Can someone help me with selecting an individual endplate when I have masked
> certain areas of the image
> <
http://imagej.1557.x6.nabble.com/file/n5004930/masked_nerve_channel.png>
>
>
>
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