change stitching background fill color?

[amaion01]

Hi-

This is my first time posting.  I'm working on a FIJI macro that bascially uses the stitching plug-in to stitch together several pictures and then threshold the image and take measurements.  However, after stitching the images together the "extra" space is filled in with black pixels.  This causes a lot of problems when I go to do the thresholding.  Is it possible to change this background fill color to another color (white or a mean pixel value)?  I haven't been able to find anything about it online, but maybe I'm not searching the right terms.

Alternatively, is there a simple/fast way to convert all black pixels in the stitched image to white/another color?  The only thing I've been able to find on this is a macro that loops through each pixel of the image and changes it if it is black.  While this would work, my images are large and I have a lot of them, so it would take a lot of time and is not ideal.

Or is there a way to adjust thresholding to ignore black pixels?  (I'm using AutoThreshold, Huang Dark because it works best on my images.)

Any other ideas or suggestions would be greatly appreciated!
Thank you!