How to select 2 channels for cell segmentation in StarDist

Hi all,
I am wandering if there is any way to select two channels (in other words two nuclear markers) simultaneously in StartDist segmentation?

In this multiplex staining FoxP3+ cell (green) completely lost DAPI(blue) signal. Two segmentation work fine separately.

Thanks in advance!

I would be a little bit careful first about whether that is real staining. The green channel (if that is what it really is) is notorious for autofluorescence from red blood cells, lipofuscin, etc. In general, I would expect the FoxP3 to either overlap with the DAPI staining or be cytoplasmic, and in your case I am not sure if it is either. Do you have a negative (secondary only, no primary) control to verify that your staining is really FoxP3?

The problem with combining the channels would likely be balancing the intensities from unrelated channels. If the staining is exclusive (and it looks like it is not always since some objects are picked up in both samples) enough, it might be better to run StarDist twice and keep both sets of results, then delete results from one that are inside cells of the second run. I would definitely verify the staining first though.

@Research_Associate thanks for your detailed feedback.
In this Opal staining this is a certainly true FoxP3 signal:
(1)AF has been subtracted,
(2) the signal is seen only in one channel with a correct nuclear localisation,
(3) these FoxP+ cells show clear cytoplasmic ring of CD45 and CD3,
(4) Also some FoxP+ cells still show traces of DAPI.
Apparently it was too strong staining to keep DAPI.

I was thinking now, if I can merge these two nuclear channels and treat them as one in Startdist. Is there any easy way to merge them directly in QuPath 0.2.2?