[ImageJ-bugs] [Bug 1025] Stitching in Fiji is not using stage coordinates from CZI correctly

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1025

Curtis Rueden <ctrueden at wisc.edu> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
                 CC|                            |ctrueden at wisc.edu
         Resolution|---                         |INVALID

--- Comment #1 from Curtis Rueden <ctrueden at wisc.edu> ---
Make sure you uncheck the "Compute overlap" option. Otherwise, the stitching
plugin tries to optimize the error of the tile overlap. When there are tiles
with very low signal, this can get weird, as you have seen.

Alternately, if you need the stitching plugin to tweak the overlap a bit, but
not too much (as is seen here), you can reduce the value of the "regression
threshold" to 0.05 from the default of 0.30, which is too high for some of this
dataset's tiles.

Arguably the behavior could be improved here to somehow guess a better
regression threshold in a contextual way -- feel free to file a feature request
on GitHub. But I expect that none of the core developers would have time to
make things more automagical any time soon. Pull requests are very, very
welcome though! :-)

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