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<body><span class="vcard"><a class="email" href="mailto:ctrueden@wisc.edu" title="Curtis Rueden <ctrueden@wisc.edu>"> <span class="fn">Curtis Rueden</span></a>
</span> changed
<a class="bz_bug_link
bz_status_RESOLVED bz_closed"
title="RESOLVED INVALID - Stitching in Fiji is not using stage coordinates from CZI correctly"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1025">bug 1025</a>
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<table border="1" cellspacing="0" cellpadding="8">
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<th>What</th>
<th>Removed</th>
<th>Added</th>
</tr>
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<td style="text-align:right;">Status</td>
<td>NEW
</td>
<td>RESOLVED
</td>
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<td style="text-align:right;">CC</td>
<td>
</td>
<td>ctrueden@wisc.edu
</td>
</tr>
<tr>
<td style="text-align:right;">Resolution</td>
<td>---
</td>
<td>INVALID
</td>
</tr></table>
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<b><a class="bz_bug_link
bz_status_RESOLVED bz_closed"
title="RESOLVED INVALID - Stitching in Fiji is not using stage coordinates from CZI correctly"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1025#c1">Comment # 1</a>
on <a class="bz_bug_link
bz_status_RESOLVED bz_closed"
title="RESOLVED INVALID - Stitching in Fiji is not using stage coordinates from CZI correctly"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1025">bug 1025</a>
from <span class="vcard"><a class="email" href="mailto:ctrueden@wisc.edu" title="Curtis Rueden <ctrueden@wisc.edu>"> <span class="fn">Curtis Rueden</span></a>
</span></b>
<pre>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! :-)</pre>
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