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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 - Threshold signed 16-bit images"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=905">905</a>
</td>
</tr>
<tr>
<th>Summary</th>
<td>Threshold signed 16-bit images
</td>
</tr>
<tr>
<th>Product</th>
<td>Fiji
</td>
</tr>
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<th>Version</th>
<td>unspecified
</td>
</tr>
<tr>
<th>Hardware</th>
<td>Macintosh
</td>
</tr>
<tr>
<th>OS</th>
<td>Mac OS
</td>
</tr>
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<th>Status</th>
<td>NEW
</td>
</tr>
<tr>
<th>Severity</th>
<td>major
</td>
</tr>
<tr>
<th>Priority</th>
<td>P5
</td>
</tr>
<tr>
<th>Component</th>
<td>ImageJ2
</td>
</tr>
<tr>
<th>Assignee</th>
<td>imagej-bugs@imagej.net
</td>
</tr>
<tr>
<th>Reporter</th>
<td>glenmac@uw.edu
</td>
</tr></table>
<p>
<div>
<pre>Created <span class=""><a href="attachment.cgi?id=199" name="attach_199" title="Huygens Pro OME XML file">attachment 199</a> <a href="attachment.cgi?id=199&action=edit" title="Huygens Pro OME XML file">[details]</a></span>
Huygens Pro OME XML file
This may be more than 1 issue.
Source files are signed 16-bit OME XML from Huygens Professional.
Opening by SCIFIO resets the histogram to 0-maximum, Bio-Formats displays the
image as -32768 to 32767 until I hit 'Reset' in B&C.
calling Threshold from menu or run("Threshold...") from macro will set by the
default method. But, checking the box for 'Stack histogram' renders the
channel black with min = 32768, max=32767 until hit 'reset' in threshold window
or B&C window. When the channel is black, moving to a different channel and
returning will restore the display but cancels the threshold.
If I run setAutoThreshold("Default dark stack"); from the macro then it sets
min = 32768, max=32767 and then all slices in the channel are masked as red.
Smetimes If I click on 'Auto', this resets with the maybe the stack histogram.
Other times I get min= -32768 and max= -max histogram (negative).
Similar results with import by Bio-Formats, although it does not make the
initial histogram reset.
I'd like to call setAutoThreshold because I can specify the stack histogram.
The run(Threshold) does not allow calling the stack histogram.
I've attached a file from Huygens.
Regards,
glen</pre>
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