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<base href="http://fiji.sc/bugzilla/" />
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<th>Bug ID</th>
<td><a class="bz_bug_link
bz_status_NEW "
title="NEW - When Fiji is launched using Miji, then the GDSC (or FindFoci) plugin is missing"
href="http://fiji.sc/bugzilla/show_bug.cgi?id=999">999</a>
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<th>Summary</th>
<td>When Fiji is launched using Miji, then the GDSC (or FindFoci) plugin is missing
</td>
</tr>
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<th>Product</th>
<td>Fiji
</td>
</tr>
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<th>Version</th>
<td>unspecified
</td>
</tr>
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<th>Hardware</th>
<td>PC
</td>
</tr>
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<th>OS</th>
<td>Windows
</td>
</tr>
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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>P4
</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>
<tr>
<th>Reporter</th>
<td>westerveld2@gmx.com
</td>
</tr>
<tr>
<th>CC</th>
<td>westerveld2@gmx.com
</td>
</tr></table>
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<pre>Dear Sir/Madam,
PROBLEM:
When I launch Fiji from Matlab using the Miji (MIJ) plugin, the GDSC plugins
(including FindFoci) do not show in the Plugins toolbar. Also, I can not run
FindFoci from a macro or from the Matlab MIJ.run() command.
DIAGNOSE:
When I launch Fiji normally, everything works fine.
I am able to start FindFoci using: Toolbar => Plugins => GDSC => FindFoci
I am able to start FindFoci using the test macro shown below.
When I launch Fiji via Matlab / Miji interface:
Run in Matlab: > Miji
The GDSC plugins including FindFoci are missing from the Toolbar => Plugins
menu.
When I start the test macro shown below, I get the error "Unrecognized command:
FindFoci"
When I start the command described in the test macro using MIJ.run(), I get the
same error "Unrecognized command: FindFoci"
Other Fiji operations work fine, e.g., MIJ.run('Invert');
Other plugins work fine, e.g., MIJ.run('Classic Watershed',
'input=131_mode9_abs mask=None use min=0 max=255');
TEST MACRO:
run("FindFoci", "mask=[None] background_method=[Std.Dev above mean]
background_parameter=3 auto_threshold=Otsu statistics_mode=Both
search_method=[Above background] search_parameter=0.30 minimum_size=5
minimum_above_saddle minimum_peak_height=[Relative above background]
peak_parameter=0.50 sort_method=[Total intensity] maximum_peaks=50
show_mask=[Peaks above saddle] fraction_parameter=0.50 show_table mark_maxima
show_peak_maxima_as_dots show_log_messages remove_edge_maxima
results_directory=[] gaussian_blur=0 centre_method=[Max value (search image)]
centre_parameter=2");
MORE DETAILS:
MIJ version: 1.3.6-fiji
When I start Miji, the following .jar packages are listed (among many others):
beansbinding-1.2.1.jar, gdsc-1.0.1-SNAPSHOT.jar
This problem was also reported on the mailing list, but I could not find it in
the bug tracker.
<a href="https://groups.google.com/forum/#!topic/fiji-devel/LefVwBOOs-g">https://groups.google.com/forum/#!topic/fiji-devel/LefVwBOOs-g</a>
Entry of Chen Huang.
Information about your version of Java:
os.arch => amd64
os.name => Windows 7
os.version => 6.1
java.version => 1.6.0_24
java.vendor => Sun Microsystems Inc.
java.runtime.name => Java(TM) SE Runtime Environment
java.runtime.version => 1.6.0_24-b07
java.vm.name => Java HotSpot(TM) 64-Bit Server VM
java.vm.version => 19.1-b02
java.vm.vendor => Sun Microsystems Inc.
java.vm.info => mixed mode
java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
java.specification.name => Java Platform API Specification
java.specification.version => 1.6
sun.cpu.endian => little
sun.desktop => windows
file.separator => \
The up-to-date check says: CHECK_TURNED_OFF
Information relevant to JAVA_HOME related problems:
JAVA_HOME is set to: C:\Wouter\Programs\Fiji.app/java/win64/jdk1.6.0_24//jre
imagej.dir => C:\Wouter\Programs\Fiji.app
Information about the version of each plugin:
Activated update sites:
ImageJ: <a href="http://update.imagej.net/">http://update.imagej.net/</a> (last check:20150122114514)
Fiji: <a href="http://fiji.sc/update/">http://fiji.sc/update/</a> (last check:20150130182536)
GDSC: <a href="http://sites.imagej.net/GDSC/">http://sites.imagej.net/GDSC/</a> (last check:20141118185052)
Files not up-to-date:
1ad3be0d (LOCAL_ONLY) 20150121082658 jars/jpedalSTD.jar
2b7aa66b (LOCAL_ONLY) 20150130115802 plugins/MorphoLibJ_-1.0.6.jar
5f60d96e (LOCAL_ONLY) 20150130135907 plugins/Watershed_.jar</pre>
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