I have two-channel image stacks in red and green that consist of large fluorescent protein structures (red) and fluorescent bacteria (green). This work is subject to a patent and I’m not able to paste the images here. However, the question is pretty straightforward.
The green channel only shows the bacteria. The red channel shows the protein and the bacteria because the bacteria are autofluorescent over a wide emission range. What I would like to do is the following:
If there is overlap between the red channel (protein) and the green channel (bacteria), convert overlapping pixels in the red channel to black pixels. This way I can remove bacteria from images where I just want to show the protein. Is there a plugin to do this, or a simple macro I can use?