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<base href="http://fiji.sc/bugzilla/" />
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<body><table border="1" cellspacing="0" cellpadding="8">
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<th>Bug ID</th>
<td><a class="bz_bug_link
bz_status_NEW "
title="NEW - Grid/Collection stitching not reading Prairie/Bruker stage location metadata"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=1109">1109</a>
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<th>Summary</th>
<td>Grid/Collection stitching not reading Prairie/Bruker stage location metadata
</td>
</tr>
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<th>Product</th>
<td>Fiji
</td>
</tr>
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<th>Version</th>
<td>unspecified
</td>
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<th>Hardware</th>
<td>PC
</td>
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<th>OS</th>
<td>Windows
</td>
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<th>Status</th>
<td>NEW
</td>
</tr>
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<th>Severity</th>
<td>normal
</td>
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<th>Priority</th>
<td>P5
</td>
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<th>Component</th>
<td>Plugins
</td>
</tr>
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<th>Assignee</th>
<td>imagej-bugs@imagej.net
</td>
</tr>
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<th>Reporter</th>
<td>thex1000@gmail.com
</td>
</tr></table>
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<div>
<pre>Created <span class=""><a href="attachment.cgi?id=253" name="attach_253" title="Sample Bruker Montage data set">attachment 253</a> <a href="attachment.cgi?id=253&action=edit" title="Sample Bruker Montage data set">[details]</a></span>
Sample Bruker Montage data set
See attached sample Bruker data set.
1. In Fiji: Plugins-> Stitching -> Grid/Collection Stitching
2. Type: Positions from file. Order: Defined by image metadata.
3. Unzip data set.
Settings for Grid Stitching
Multi series file: Choose AtlasVolume-07072015-0914-008.xml
Invert X coordinates checked
Invert Y coordinates unchecked
Compute overlap unchecked. This forces the plugin to read in coordinates.
4. Click OK.
In the log window, the positions are read in as 0.0 instead of the actual stage
locations and the resulting stitched image is incorrect.
Other settings that do not matter as much:
Fusion method: linear Blending
Regression th: 0.3
Max/avg displacement th: 2.50
Absolute displacement th: 3.50
Add tiles as ROIs unchecked
Ignore calibration unchecked
Invert z stage position unchecked
subpixel accuracy checked
downsample tiles unchecked
display fusion unchecked
use virtual images unchecked
computation parameters: save memory
image output: fuse and display</pre>
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