Is it possible to get Hugin to prioritize images with higher 
detail/sharpness when stitching?

I recently started doing photomicrographic panoramas using a reversed lens 
setup and a 3-axis stage. Overall, my results are good, I have adequate 
resolution into the 5μm range. Initially I tried to use CaptureOne to merge 
my photos to a DNG but I ran into its upper size limit (715mp) and I'm 
working with Hugin now for the larger ones.

I have learned how to get excellent alignment, clean up bad points, 
optimize, and output to bigtiff/non-ZFW compression so that I don't exceed 
the 4gb TIF file limit.

After all that, I finally have an image I can view in Photoshop and while 
the stitch looks clean, I can tell that Hugin is not prioritizing images 
with greater sharpness because I must've shifted something during the set 
and some images are a little out of focus.

I have looked and can't find any option in the GUI to get Hugin to 
prioritize sharper images. I found some potentially out of date references 
to setting contrast or entropy weighting, but particularly for entropy, I 
am not quite sure what it does.

Would one of those or another option achieve the result I want? Or is there 
a way to have Hugin treat it is a focus stack+panorama so it will 
prioritize the photo of greatest detail?

Any help would be great! I will also be trying these options myself, but 
with each run taking around 1hr to complete, it will be slow going (hence 
taking the time to ask for help!)

-- 
A list of frequently asked questions is available at: 
http://wiki.panotools.org/Hugin_FAQ
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