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Bug 745 - Different output file after update
Different output file after update
Status: NEEDSINFO
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Other Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-05-08 12:31 CDT by Christopher Schmied
Modified: 2014-07-14 12:10 CDT
2 users (show)

See Also:
Description Christopher Schmied 2014-05-08 12:31:43 CDT 
Dear Fiji developers,

We are running Fiji with a virtual frame buffer on a cluster (CentOS 6.3) using the following scripts:

http://fiji.sc/SPIM_Registration_on_cluster

We assessed the performance of the processing via the SPIM Registration plugins by the output files of this processing. Which in the past contained the logfile of the plugin. After recent updates this output file does not contain the log file of the plugin anymore. It contains what looks like an ouput of Fiji itself. 

We are now unfortunatly unable to judge the success of the plugins properly. We would be very grateful if the previous state could be reinstated or if you could find a workaround. 

Below you see examples of the output file before and after the update:

Output before update:

Sender: LSF System <hpcadmin@n11>
Subject: Job 466652: <./register-3.job> in cluster scuba_cluster1 Done

Job <./register-3.job> was submitted from host <madmax> by user <schmied> in cluster <scuba_cluster1>.
Job was executed on host(s) <n11>, in queue <short>, as user <schmied> in cluster <scuba_cluster1>.
</home/schmied> was used as the home directory.
</projects/tomancak_lightsheet/Christopher/Test_scripts/single_channel/jobs/registration> was used as the working directory.
Started at Tue Feb 18 17:05:20 2014
Results reported at Tue Feb 18 17:07:03 2014

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
./register-3.job
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    395.05 sec.
    Max Memory :      6765 MB
    Max Swap   :     85421 MB

    Max Processes  :         6
    Max Threads    :        44

The output (if any) follows:

12 cores available for multi-threading
type_of_registration=Single-channel
pattern_of_spim=spim_TL{t}_Angle{a}.tif
transformation_model=Affine
dir=/projects/tomancak_lightsheet/Christopher/Test_scripts/single_channel/
timepoint=3
angles=1,2,3,4,5
xy_resolution=1
z_resolution=3.481975
radius1=2
radius2=3
threshold=0.0070
init Bead_Registration dialog: tfSpimDataDirectory.getText() = 
ChannelPattern: 
Channels: (0)
ChannelsToRegister: 
ChannelsRegister: (0)
ChannelsToFuse: 
ChannelsFuse: (0)
Version 0.55
Using model: mpicbg.models.AffineModel3D
(Tue Feb 18 17:05:26 CET 2014): Starting Bead Extraction
(Tue Feb 18 17:05:26 CET 2014): Starting Integral Image based DOM Bead Extraction for spim_TL3_Angle1.tif
(Tue Feb 18 17:05:26 CET 2014): Opening '/projects/tomancak_lightsheet/Christopher/Test_scripts/single_channel/spim_TL3_Angle1.tif' [ArrayContainerFactory]
log4j:WARN No appenders could be found for logger (loci.common.services.ServiceFactory).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Opening '/projects/tomancak_lightsheet/Christopher/Test_scripts/single_channel/spim_TL3_Angle1.tif' [1920x1200x141 type=uint16 image=Image<FloatType>]
LOCI.openLOCI(): Cannot read metadata, setting calibration to 1
(Tue Feb 18 17:05:34 CET 2014): Computing Integral Image
(Tue Feb 18 17:05:39 CET 2014): min intensity = 142.0, max intensity = 19972.0
(Tue Feb 18 17:05:39 CET 2014): Computing Difference-of-Mean
(Tue Feb 18 17:05:43 CET 2014): Extracting peaks
(Tue Feb 18 17:05:47 CET 2014): Subpixel localization using quadratic n-dimensional fit
Found peaks (possible beads): 25954 in view spim_TL3_Angle1.tif
(Tue Feb 18 17:05:48 CET 2014): Starting Integral Image based DOM Bead Extraction for spim_TL3_Angle2.tif
(Tue Feb 18 17:05:48 CET 2014): Opening '/projects/tomancak_lightsheet/Christopher/Test_scripts/single_channel/spim_TL3_Angle2.tif' [ArrayContainerFactory]
Opening '/projects/tomancak_lightsheet/Christopher/Test_scripts/single_channel/spim_TL3_Angle2.tif' [1920x1200x141 type=uint16 image=Image<FloatType>]
LOCI.openLOCI(): Cannot read metadata, setting calibration to 1
(Tue Feb 18 17:05:56 CET 2014): Computing Integral Image
(Tue Feb 18 17:05:58 CET 2014): min intensity = 136.0, max intensity = 21545.0
(Tue Feb 18 17:05:58 CET 2014): Computing Difference-of-Mean
(Tue Feb 18 17:06:02 CET 2014): Extracting peaks
(Tue Feb 18 17:06:06 CET 2014): Subpixel localization using quadratic n-dimensional fit
Found peaks (possible beads): 22592 in view spim_TL3_Angle2.tif
(Tue Feb 18 17:06:06 CET 2014): Starting Integral Image based DOM Bead Extraction for spim_TL3_Angle3.tif
(Tue Feb 18 17:06:06 CET 2014): Opening '/projects/tomancak_lightsheet/Christopher/Test_scripts/single_channel/spim_TL3_Angle3.tif' [ArrayContainerFactory]
Opening '/projects/tomancak_lightsheet/Christopher/Test_scripts/single_channel/spim_TL3_Angle3.tif' [1920x1200x141 type=uint16 image=Image<FloatType>]
LOCI.openLOCI(): Cannot read metadata, setting calibration to 1
(Tue Feb 18 17:06:11 CET 2014): Computing Integral Image
(Tue Feb 18 17:06:13 CET 2014): min intensity = 0.0, max intensity = 21405.0
(Tue Feb 18 17:06:13 CET 2014): Computing Difference-of-Mean
(Tue Feb 18 17:06:16 CET 2014): Extracting peaks
(Tue Feb 18 17:06:20 CET 2014): Subpixel localization using quadratic n-dimensional fit
Found peaks (possible beads): 27032 in view spim_TL3_Angle3.tif
(Tue Feb 18 17:06:20 CET 2014): Starting Integral Image based DOM Bead Extraction for spim_TL3_Angle4.tif
(Tue Feb 18 17:06:20 CET 2014): Opening '/projects/tomancak_lightsheet/Christopher/Test_scripts/single_channel/spim_TL3_Angle4.tif' [ArrayContainerFactory]
Opening '/projects/tomancak_lightsheet/Christopher/Test_scripts/single_channel/spim_TL3_Angle4.tif' [1920x1200x141 type=uint16 image=Image<FloatType>]
LOCI.openLOCI(): Cannot read metadata, setting calibration to 1
(Tue Feb 18 17:06:27 CET 2014): Computing Integral Image
(Tue Feb 18 17:06:31 CET 2014): min intensity = 0.0, max intensity = 20666.0
(Tue Feb 18 17:06:31 CET 2014): Computing Difference-of-Mean
(Tue Feb 18 17:06:34 CET 2014): Extracting peaks
(Tue Feb 18 17:06:40 CET 2014): Subpixel localization using quadratic n-dimensional fit
Found peaks (possible beads): 42694 in view spim_TL3_Angle4.tif
(Tue Feb 18 17:06:40 CET 2014): Starting Integral Image based DOM Bead Extraction for spim_TL3_Angle5.tif
(Tue Feb 18 17:06:40 CET 2014): Opening '/projects/tomancak_lightsheet/Christopher/Test_scripts/single_channel/spim_TL3_Angle5.tif' [ArrayContainerFactory]
Opening '/projects/tomancak_lightsheet/Christopher/Test_scripts/single_channel/spim_TL3_Angle5.tif' [1920x1200x142 type=uint16 image=Image<FloatType>]
LOCI.openLOCI(): Cannot read metadata, setting calibration to 1
(Tue Feb 18 17:06:46 CET 2014): Computing Integral Image
(Tue Feb 18 17:06:49 CET 2014): min intensity = 143.0, max intensity = 23491.0
(Tue Feb 18 17:06:49 CET 2014): Computing Difference-of-Mean
(Tue Feb 18 17:06:51 CET 2014): Extracting peaks
(Tue Feb 18 17:06:55 CET 2014): Subpixel localization using quadratic n-dimensional fit
Found peaks (possible beads): 24320 in view spim_TL3_Angle5.tif
Opening files took: 34 sec (39 %)
Computation took: 53 sec (61 %)
(Tue Feb 18 17:06:55 CET 2014): Finished Bead Extraction
(Tue Feb 18 17:06:55 CET 2014): Starting Registration
spim_TL3_Angle2.tif<->spim_TL3_Angle5.tif: Remaining inliers after RANSAC: 160 of 195 (82%) with average error 0.7164947547484192
spim_TL3_Angle2.tif<->spim_TL3_Angle3.tif: Remaining inliers after RANSAC: 145 of 173 (84%) with average error 1.0101229504264642
spim_TL3_Angle1.tif<->spim_TL3_Angle2.tif: Remaining inliers after RANSAC: 110 of 150 (73%) with average error 0.9546123465353792
spim_TL3_Angle3.tif<->spim_TL3_Angle5.tif: Remaining inliers after RANSAC: 16 of 59 (27%) with average error 0.3524021739140153
spim_TL3_Angle1.tif<->spim_TL3_Angle5.tif: Remaining inliers after RANSAC: 92 of 144 (64%) with average error 0.8370325414706832
spim_TL3_Angle1.tif<->spim_TL3_Angle3.tif: Remaining inliers after RANSAC: 154 of 186 (83%) with average error 0.6880853004366546
spim_TL3_Angle2.tif<->spim_TL3_Angle4.tif: Remaining inliers after RANSAC: 95 of 121 (79%) with average error 0.7090062948433976
spim_TL3_Angle4.tif<->spim_TL3_Angle5.tif: Remaining inliers after RANSAC: 55 of 142 (39%) with average error 0.4513551210137931
spim_TL3_Angle1.tif<->spim_TL3_Angle4.tif: Remaining inliers after RANSAC: 128 of 175 (73%) with average error 0.5806687898584644
spim_TL3_Angle3.tif<->spim_TL3_Angle4.tif: Remaining inliers after RANSAC: 55 of 129 (43%) with average error 0.857222831249237
spim_TL3_Angle1.tif (id = 0) has 484 correspondences in 4 other views.
spim_TL3_Angle2.tif (id = 1) has 510 correspondences in 4 other views.
spim_TL3_Angle3.tif (id = 2) has 370 correspondences in 4 other views.
spim_TL3_Angle4.tif (id = 3) has 333 correspondences in 4 other views.
spim_TL3_Angle5.tif (id = 4) has 323 correspondences in 4 other views.
The total number of detections was: 142592
The total number of correspondence candidates was: 1474
The total number of true correspondences is: 1010
Fixing tile spim_TL3_Angle1.tif (id = 0)
Successfully optimized configuration of 5 tiles after 282 iterations:
  average displacement: 1.301px
  minimal displacement: 1.126px
  maximal displacement: 1.501px
Optimizer Matrices
spim_TL3_Angle1.tif (id = 0):
Transformation:
3d-affine: (1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0)
Scaling: (1.0, 1.0, 1.0)
spim_TL3_Angle2.tif (id = 1):
Transformation:
3d-affine: (1.0001096, -0.0051788427, -0.0048389137, 6.7142754, -0.0035283389, 0.30462265, -0.9485754, 459.96497, 0.0058890777, 0.95343184, 0.31159014, -549.583)
Scaling: (1.0001496037292668, 0.9953995861339521, 1.0039461236452363)
spim_TL3_Angle3.tif (id = 2):
Transformation:
3d-affine: (1.0000328, -0.011610292, -4.2062998E-4, 9.615857, -0.01004544, -0.8112623, -0.5879747, 1112.0059, 0.0053530782, 0.5897829, -0.80761087, -277.8199)
Scaling: (1.0003442565657652, 0.9986946135710281, 1.0030904935191043)
spim_TL3_Angle4.tif (id = 3):
Transformation:
3d-affine: (0.9998945, -0.010100707, 0.0069042444, 8.820425, -0.011368095, -0.80696166, 0.5884241, 1074.4827, -0.0031039603, -0.5895192, -0.8162052, 439.39343)
Scaling: (0.9996990531929825, 1.0076983158789519, 0.9981870179835688)
spim_TL3_Angle5.tif (id = 4):
Transformation:
3d-affine: (1.0000212, -0.00287015, 0.0068382025, 6.435096, -0.00419832, 0.31431904, 0.9613035, 302.54315, -0.005504055, -0.9541971, 0.3082497, 599.18884)
Scaling: (0.999983191084947, 1.011795860334464, 1.002426529976938)
(Tue Feb 18 17:07:01 CET 2014): Finished Registration
Finished processing.


PS:

Read file <err.466652> for stderr output of this job.





Output file after update: 


Sender: LSF System <hpcadmin@n41>
Subject: Job 54074: <./register-10.job> in cluster scuba_cluster1 Done

Job <./register-10.job> was submitted from host <madmax> by user <schmied> in cluster <scuba_cluster1>.
Job was executed on host(s) <n41>, in queue <short>, as user <schmied> in cluster <scuba_cluster1>.
</home/schmied> was used as the home directory.
</projects/pilot_spim/Christopher/pipeline/jobs_master_beta_2.0/registration> was used as the working directory.
Started at Thu Apr 24 18:20:52 2014
Results reported at Thu Apr 24 18:22:08 2014

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
./register-10.job
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    328.78 sec.
    Max Memory :      6408 MB
    Max Swap   :     89420 MB

    Max Processes  :         6
    Max Threads    :        48

The output (if any) follows:

12 cores available for multi-threading
type_of_registration=Single-channel
type_of_detection=Difference-of-Mean (Integral image based)
dir=/projects/pilot_spim/Christopher/2014-04-22_Stock19_Stock17_2/
pattern_of_spim=spim_TL{tt}_Angle{a}_Channel1.tif
timepoint=10
angles=1,2,3,4,5
bead_brightness=Advanced ...
subpixel_localization=3-dimensional quadratic fit (all detections)
xy_resolution=1
z_resolution=3.4482758
transformation_model=Affine
imglib_container=Array container (images smaller ~2048x2048x450 px)
radius1=2
radius2=3
threshold=0.01
initial_sigma=void
threshold_gaussian=void
[INFO] Created service: org.scijava.log.StderrLogService
[INFO] Created service: org.scijava.thread.DefaultThreadService
[INFO] Created service: org.scijava.event.DefaultEventService
[INFO] Found 1096 plugins.
[WARNING] 1 exceptions occurred during plugin discovery.
[INFO] Created service: org.scijava.plugin.DefaultPluginService
log4j:WARN No appenders could be found for logger (org.bushe.swing.event.EventService).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
[INFO] Created service: org.scijava.object.DefaultObjectService
[INFO] Created service: imagej.module.DefaultModuleService
[INFO] Created service: imagej.command.DefaultCommandService
[INFO] Created service: imagej.script.DefaultScriptService
[INFO] Created service: io.scif.services.DefaultFormatService
[INFO] Found 22 DataType plugins.
[INFO] Created service: imagej.data.types.DefaultDataTypeService
[INFO] Created service: imagej.data.DefaultDatasetService
[INFO] Created service: imagej.display.DefaultDisplayService
[INFO] Created service: imagej.data.display.DefaultImageDisplayService
[INFO] Created service: imagej.data.lut.DefaultLUTService
[INFO] Created service: imagej.console.DefaultConsoleService
[INFO] Created service: imagej.io.DefaultIOService
[INFO] Created service: imagej.io.DefaultRecentFileService
[INFO] Created service: imagej.menu.DefaultMenuService
[INFO] Created service: imagej.options.DefaultOptionsService
[INFO] Created service: imagej.plugins.commands.app.CoreAppEventService
[INFO] Found 2 Platform plugins.
[INFO] Configuring platform: imagej.platform.DefaultPlatform
[INFO] Configuring platform: imagej.platform.DefaultPlatform
[INFO] Created service: imagej.platform.DefaultPlatformService
[INFO] Created service: imagej.text.DefaultTextService
[INFO] Found 3 applications.
[INFO] Created service: org.scijava.app.DefaultAppService
[INFO] Created service: org.scijava.app.DefaultStatusService
[INFO] Created service: imagej.tool.DefaultToolService
[INFO] Found 26 InputWidget plugins.
[INFO] Created service: imagej.widget.DefaultWidgetService
[INFO] Created service: org.scijava.event.DefaultEventHistory
[INFO] Created service: imagej.updater.core.DefaultUploaderService
[INFO] Created service: net.imglib2.meta.units.DefaultUnitService
[INFO] Created service: imagej.data.animation.DefaultAnimationService
[INFO] Created service: imagej.data.autoscale.DefaultAutoscaleService
[INFO] Created service: imagej.data.DefaultImgPlusService
[INFO] Created service: imagej.data.display.DefaultInputService
[INFO] Created service: imagej.ui.common.awt.AWTRenderingService
[INFO] Created service: imagej.data.display.DefaultOverlayService
[INFO] Created service: imagej.data.display.DefaultWindowService
[INFO] Created service: imagej.data.display.DefaultZoomService
[INFO] Created service: imagej.data.measure.DefaultMeasurementService
[INFO] Created service: imagej.data.measure.DefaultStatisticsService
[INFO] Created service: imagej.data.operator.DefaultCalculatorService
[INFO] Created service: imagej.data.sampler.DefaultSamplerService
[INFO] Created service: imagej.data.threshold.DefaultThresholdService
[INFO] Created service: imagej.ui.dnd.DefaultDragAndDropService
[INFO] Created service: imagej.ui.DefaultUIService
[INFO] Created service: imagej.plugins.uis.swing.SwingIconService
[INFO] Created service: imagej.plugins.uis.swing.overlay.JHotDrawService
[INFO] Created service: imagej.plugins.commands.restructure.SplitChannelsContextMonitor
[INFO] Created service: imagej.ui.common.awt.AWTScreenCaptureService
[INFO] Created service: io.scif.ome.services.DefaultOMEXMLService
[INFO] Created service: io.scif.ome.services.DefaultOMEMetadataService
[INFO] Created service: io.scif.codec.DefaultCodecService
[INFO] Created service: io.scif.DefaultMetadataService
[INFO] Created service: io.scif.formats.qt.DefaultQTJavaService
[INFO] Created service: io.scif.formats.tiff.DefaultTiffService
[INFO] Created service: io.scif.gui.DefaultGUIService
[INFO] Created service: io.scif.refs.DefaultRefManagerService
[INFO] Created service: io.scif.img.cell.cache.MapDBCache
[INFO] Created service: io.scif.img.converters.DefaultPlaneConverterService
[INFO] Created service: io.scif.img.DefaultImgUtilityService
[INFO] Created service: io.scif.io.DefaultNIOService
[INFO] Created service: io.scif.services.DefaultFilePatternService
[INFO] Created service: io.scif.services.DefaultLocationService
[INFO] Created service: io.scif.services.DefaultTranslatorService
[INFO] Created service: io.scif.services.JAIIIOServiceImpl
[INFO] Created service: io.scif.xml.DefaultXMLService
[INFO] Found 0 scripts
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > AND...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > AND...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: label='About ImageJ...', menu='Help > About ImageJ...', iconPath='/icons/commands/information.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: label='About ImageJ...', menu='Help > About ImageJ...', iconPath='/icons/commands/information.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Abs...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Abs...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Noise Reduction > Adaptive Median', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Noise Reduction > Adaptive Median', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Axes > Add Axis...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Axes > Add Axis...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Data > Add Data...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Data > Add Data...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Overlay > Add Image', iconPath='/icons/commands/bricks.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Overlay > Add Image', iconPath='/icons/commands/bricks.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Add Noise...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Add Noise...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Add Specified Noise...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Add Specified Noise...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Add...', iconPath='/icons/commands/sum.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Add...', iconPath='/icons/commands/sum.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Noise Reduction > Alpha Trimmed Mean', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Noise Reduction > Alpha Trimmed Mean', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Animation > Animation Options...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Animation > Animation Options...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Appearance...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Appearance...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Arrow Tool...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Arrow Tool...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Adjust > Auto-Contrast', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Adjust > Auto-Contrast', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Axes > Axis Position Backward', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Axes > Axis Position Backward', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Axes > Axis Position Forward', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Axes > Axis Position Forward', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Utilities > Benchmark', iconPath='/icons/commands/bricks.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Utilities > Benchmark', iconPath='/icons/commands/bricks.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Transform > Bin...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Transform > Bin...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Binary > Binarize...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Binary > Binarize...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Adjust > Brightness/Contrast...', iconPath='/icons/commands/contrast.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Adjust > Brightness/Contrast...', iconPath='/icons/commands/contrast.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Sandbox > Button Demo', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Sandbox > Button Demo', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Utilities > Capture Image', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Utilities > Capture Image', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Utilities > Capture Screen', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Utilities > Capture Screen', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Type > Change...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Type > Change...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Color > Channels Tool...', iconPath='/icons/commands/color_wheel.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Color > Channels Tool...', iconPath='/icons/commands/color_wheel.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Channels...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Channels...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: label='Clear Recent', menu='File > Open Recent > Clear List', priority=0.0, enabled=true, pluginType=Command
	 ignored: label='Clear Recent', menu='File > Open Recent > Clear List', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Binary > Close', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Binary > Close', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='File > Close', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='File > Close', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='File > Close All', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='File > Close All', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Compatibility...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Compatibility...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Compiler...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Compiler...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Noise Reduction > Contraharmonic Mean', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Noise Reduction > Contraharmonic Mean', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Conversions...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Conversions...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Copy To System', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Copy To System', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Binary > Create Mask...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Binary > Create Mask...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Shortcuts > Create Shortcut...', iconPath='/icons/commands/bricks.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Shortcuts > Create Shortcut...', iconPath='/icons/commands/bricks.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Crop', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Crop', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > DICOM...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > DICOM...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: label='Default Overlay Settings', menu='Image > Overlay > Overlay Options...', priority=0.0, enabled=true, pluginType=Command
	 ignored: label='Default Overlay Settings', menu='Image > Overlay > Overlay Options...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Axes > Delete Axis...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Axes > Delete Axis...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Data > Delete Data...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Data > Delete Data...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Adjust > Delete Threshold', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Adjust > Delete Threshold', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Selection > Deselect Overlays', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Selection > Deselect Overlays', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Sandbox > Dialog Prompt Demo', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Sandbox > Dialog Prompt Demo', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Binary > Dilate', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Binary > Dilate', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Divide...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Divide...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Debug > Dump Stack', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Debug > Dump Stack', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Duplicate', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Duplicate', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Shadows > East', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Shadows > East', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Axes > Edit Axes...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Axes > Edit Axes...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Equation...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Equation...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Binary > Erode', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Binary > Erode', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Exp...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Exp...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Fill', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Fill', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Utilities > Find Commands...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Utilities > Find Commands...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Find Edges', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Find Edges', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Overlay > Flatten', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Overlay > Flatten', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Transform > Flip Axis', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Transform > Flip Axis', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Transform > Flip Horizontally', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Transform > Flip Horizontally', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Transform > Flip Vertically', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Transform > Flip Vertically', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Fonts...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Fonts...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Overlay > From Overlay Manager', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Overlay > From Overlay Manager', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Gamma...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Gamma...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Filters > Gaussian Blur...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Filters > Gaussian Blur...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Noise Reduction > Geometric Mean', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Noise Reduction > Geometric Mean', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Noise Reduction > Harmonic Mean', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Noise Reduction > Harmonic Mean', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Analyze > Histogram Plot', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Analyze > Histogram Plot', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Image Calculator...', iconPath='/icons/commands/calculator.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Image Calculator...', iconPath='/icons/commands/calculator.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Help > ImageJ Website...', iconPath='/icons/commands/world_link.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Help > ImageJ Website...', iconPath='/icons/commands/world_link.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Input/Output...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Input/Output...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Debug > Inspect Image', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Debug > Inspect Image', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Debug > Inspect Objects', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Debug > Inspect Objects', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Debug > Invalid Command', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Debug > Invalid Command', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Invert...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Invert...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: label='LUT Selector', menu='Image > Lookup Tables > Select...', priority=0.0, enabled=true, pluginType=Command
	 ignored: label='LUT Selector', menu='Image > Lookup Tables > Select...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Overlay > Labels...', iconPath='/icons/commands/bricks.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Overlay > Labels...', iconPath='/icons/commands/bricks.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Line Width...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Line Width...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Shortcuts > List Shortcuts...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Shortcuts > List Shortcuts...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Log...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Log...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Look and Feel...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Look and Feel...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Binary > Make Binary...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Binary > Make Binary...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Binary > Make Mask Overlay...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Binary > Make Mask Overlay...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Sandbox > Mandelbrot Set', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Sandbox > Mandelbrot Set', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Max...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Max...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Noise Reduction > Maximum', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Noise Reduction > Maximum', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Noise Reduction > Mean', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Noise Reduction > Mean', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Sandbox > Measurement Demo', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Sandbox > Measurement Demo', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Noise Reduction > Median', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Noise Reduction > Median', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Memory & Threads...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Memory & Threads...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Noise Reduction > Midpoint', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Noise Reduction > Midpoint', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Min...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Min...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Noise Reduction > Minimum', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Noise Reduction > Minimum', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Misc...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Misc...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Sandbox > Mixed World Command', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Sandbox > Mixed World Command', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Sandbox > Multidimensional Test Image', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Sandbox > Multidimensional Test Image', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Multiply...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Multiply...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > NaN Background', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > NaN Background', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: label='New Image...', menu='File > New > Image...', iconPath='/icons/commands/picture.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: label='New Image...', menu='File > New > Image...', iconPath='/icons/commands/picture.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Shadows > North', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Shadows > North', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Shadows > Northeast', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Shadows > Northeast', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Shadows > Northwest', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Shadows > Northwest', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > OR...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > OR...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Binary > Open', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Binary > Open', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='File > Open...', iconPath='/icons/commands/folder_picture.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='File > Open...', iconPath='/icons/commands/folder_picture.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Zoom > Original Scale', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Zoom > Original Scale', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Stacks > Orthogonal Views', iconPath='/icons/commands/bricks.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Stacks > Orthogonal Views', iconPath='/icons/commands/bricks.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Overlay > Overlay Manager', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Overlay > Overlay Manager', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: label='Overlay Properties...', menu='Image > Overlay > Properties...', priority=0.0, enabled=true, pluginType=Command
	 ignored: label='Overlay Properties...', menu='Image > Overlay > Properties...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Sandbox > Parameter Assignment Order', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Sandbox > Parameter Assignment Order', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Point Tool...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Point Tool...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Sandbox > PointSet Demo', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Sandbox > PointSet Demo', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Power...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Power...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: label='Preferences', menu='File > Preferences', priority=0.0, enabled=true, pluginType=Command
	 ignored: label='Preferences', menu='File > Preferences', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Profile Plot Options...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Profile Plot Options...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Proxy Settings...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Proxy Settings...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: label='Quit', menu='File > Quit', iconPath='/icons/commands/door_in.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: label='Quit', menu='File > Quit', iconPath='/icons/commands/door_in.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Reciprocal...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Reciprocal...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Macros > Record...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Macros > Record...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Overlay > Remove Overlay', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Overlay > Remove Overlay', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Overlay > Remove Overlay References', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Overlay > Remove Overlay References', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Axes > Reorder Axis', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Axes > Reorder Axis', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Data > Reorder Data...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Data > Reorder Data...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Reset', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Reset', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Adjust > Resize...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Adjust > Resize...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Stacks > Reslice...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Stacks > Reslice...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='File > Revert', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='File > Revert', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Transform > Rotate 90 Degrees Left', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Transform > Rotate 90 Degrees Left', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Transform > Rotate 90 Degrees Right', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Transform > Rotate 90 Degrees Right', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Transform > Rotate...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Transform > Rotate...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Rounded Rect Tool...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Rounded Rect Tool...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Run Script...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Run Script...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Salt and Pepper', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Salt and Pepper', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='File > Save', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='File > Save', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='File > Save As...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='File > Save As...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='File > New > Script...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='File > New > Script...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Selection > Select Overlays', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Selection > Select Overlays', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Selection > Select View', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Selection > Select View', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Axes > Set Active Axis...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Axes > Set Active Axis...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Axes > Set Axis Position...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Axes > Set Axis Position...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: label='Set Zoom...', menu='Image > Zoom > Set...', priority=0.0, enabled=true, pluginType=Command
	 ignored: label='Set Zoom...', menu='Image > Zoom > Set...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Set...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Set...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Shadows > Shadows Demo', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Shadows > Shadows Demo', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Sharpen', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Sharpen', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Show Info...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Show Info...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Color > Show LUT', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Color > Show LUT', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Color > Show LUT As Table', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Color > Show LUT As Table', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Smooth', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Smooth', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Shadows > South', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Shadows > South', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Shadows > Southeast', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Shadows > Southeast', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Shadows > Southwest', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Shadows > Southwest', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Selection > Specify...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Selection > Specify...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Color > Spectral Composite...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Color > Spectral Composite...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Square Root...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Square Root...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Square...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Square...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Animation > Start Animation', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Animation > Start Animation', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Sandbox > Statistics Demo', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Sandbox > Statistics Demo', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Animation > Stop All Animations', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Animation > Stop All Animations', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Animation > Stop Animation', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Animation > Stop Animation', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Debug > Subscribers', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Debug > Subscribers', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > Subtract...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > Subtract...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Help > Switch to Legacy Mode', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Help > Switch to Legacy Mode', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Analyze > Tools > Synchronize Windows', iconPath='/icons/commands/bricks.png', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Analyze > Tools > Synchronize Windows', iconPath='/icons/commands/bricks.png', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Debug > System Information', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Debug > System Information', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Sandbox > Table Demo', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Sandbox > Table Demo', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Sandbox > TextDisplayTest', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Sandbox > TextDisplayTest', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Adjust > Threshold...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Adjust > Threshold...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Window > Tile Vertical', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Window > Tile Vertical', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Zoom > To Selection', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Zoom > To Selection', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Transform > Translate...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Transform > Translate...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Noise > Noise Reduction > Trimmed Mean', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Noise > Noise Reduction > Trimmed Mean', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Help > Update...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Help > Update...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Help > Upload Sample Image', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Help > Upload Sample Image', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Image > Zoom > View 100%', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Image > Zoom > View 100%', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Edit > Options > Wand Tool...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Edit > Options > Wand Tool...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Plugins > Debug > Watch Events', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Plugins > Debug > Watch Events', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Shadows > West', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Shadows > West', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Process > Math > XOR...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Process > Math > XOR...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: label='Zoom In', menu='Image > Zoom > In', priority=0.0, enabled=true, pluginType=Command
	 ignored: label='Zoom In', menu='Image > Zoom > In', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: label='Zoom Out', menu='Image > Zoom > Out', priority=0.0, enabled=true, pluginType=Command
	 ignored: label='Zoom Out', menu='Image > Zoom > Out', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Duplicate...', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Duplicate...', priority=0.0, enabled=true, pluginType=Command
[WARNING] ShadowMenu: menu item already exists:
	existing: menu='Split Channels', priority=0.0, enabled=true, pluginType=Command
	 ignored: menu='Split Channels', priority=0.0, enabled=true, pluginType=Command
[WARNING] Overridden plugin ij.plugin.AboutBox is blacklisted
[WARNING] Overridden plugin ij.plugin.LutLoader("3-3-2 RGB") is blacklisted
[WARNING] Overridden plugin ij.plugin.Commands("quit") is blacklisted
[INFO] Found 648 legacy plugins (plus 147 ignored).
[INFO] Created service: imagej.legacy.DefaultLegacyService
[INFO] Created service: imagej.render.DummyRenderingService
[INFO] Created service: imagej.data.display.DummyScreenCaptureService
[INFO] Created service: io.scif.services.DefaultInitializeService
init Bead_Registration dialog: tfSpimDataDirectory.getText() = 
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/lustre/sw/users/tomancak/packages/Fiji.app/jars/slf4j-log4j12-1.7.2.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/lustre/sw/users/tomancak/packages/Fiji.app/jars/logback-classic-1.0.9.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
Opening '/projects/pilot_spim/Christopher/2014-04-22_Stock19_Stock17_2/spim_TL10_Angle1_Channel1.tif' [1920x1200x131 type=uint16 image=Image<FloatType>]
LOCI.openLOCI(): Cannot read metadata, setting calibration to 1
Opening '/projects/pilot_spim/Christopher/2014-04-22_Stock19_Stock17_2/spim_TL10_Angle2_Channel1.tif' [1920x1200x131 type=uint16 image=Image<FloatType>]
LOCI.openLOCI(): Cannot read metadata, setting calibration to 1
Opening '/projects/pilot_spim/Christopher/2014-04-22_Stock19_Stock17_2/spim_TL10_Angle3_Channel1.tif' [1920x1200x131 type=uint16 image=Image<FloatType>]
LOCI.openLOCI(): Cannot read metadata, setting calibration to 1
Opening '/projects/pilot_spim/Christopher/2014-04-22_Stock19_Stock17_2/spim_TL10_Angle4_Channel1.tif' [1920x1200x131 type=uint16 image=Image<FloatType>]
LOCI.openLOCI(): Cannot read metadata, setting calibration to 1
Opening '/projects/pilot_spim/Christopher/2014-04-22_Stock19_Stock17_2/spim_TL10_Angle5_Channel1.tif' [1920x1200x131 type=uint16 image=Image<FloatType>]
LOCI.openLOCI(): Cannot read metadata, setting calibration to 1


PS:

Read file <err.54074> for stderr output of this job.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.8.5
  java.version => 1.6.0_51
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_51-b11-457-11M4509
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.51-b01-457
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  ij.dir => /Applications/Fiji.app

Information about the version of each plugin:

  4ccfd999:554f1fa4:387faf3d 20131011135733 :00c8c9c
  2c93d9a6:2d9d2593:be71a9c0 20130806174337 :00efaa6
  9770ed7e:40cf929f:0606b3ee 20130524113940 :011890f
  426d64f4:be49972e:be49972e 20131011135747 :0307564
  8c8f6d33:ac4c137b:ac4c137b 20130806174352 :0326851
  692e9eb1:07386943:28b8e02e 20130822143713 :040d0ea
  6cfb774f:b8f734bb:b8f734bb 20131203105121 :04478f7
  24590873:d3ccdd03:d3ccdd03 20130414235049 :044f3fe
  015d8a2e:9cbf5db5:8de91f6b 20130812143252 :04782f0
  6738a701:d6932866:d6932866 20130806174349 :04a4a5c
  6bd9ca65:0954132b:637e808e 20140328093436 :05b1de4
  30420365:5a23ed73:5a23ed73 20130414235049 :069ebf3
  84d76592:53d3f4e0:53d3f4e0 20130414235049 :06c89a7
  3f876cb1:205f633a:205f633a 20130414235049 :07e9a49
  08453207:08453207:08453207 20130414235049 :0845320
  a058419c:e976dd2f:0194333b 20140328093521 :08a4dae
  3ea9130d:791596f0:791596f0 20140328093511 :096abf5
  09868b51:09868b51:09868b51 20130414235049 :09868b5
  fb827967:5dbb3afe:1bf26607 20140328093438 :0a5d89f
  0a93f0be:0a93f0be:0a93f0be 20130414235049 :0a93f0b
  cd9eda33:239d2a49:f25c125a 20130414235049 :0b76869
  61ab84fd:2a4992aa:2a4992aa 20130806174354 :0bd5f17
  283a7027:9263e996:9263e996 20130414235049 :0c2a5e1
  e7eda3a9:fb7edd8b:fb7edd8b 20140425104150 :0cc89d6
  230a6703:f7855a25:ab973b1e 20130822143712 :0d229f1
  72ea2fc2:73af3a23:73af3a23 20130524114005 :0d4057e
  2335d2f7:425d0ca9:39c6a187 20140328093426 :0d70010
  6478da40:1d98f525:1d98f525 20130414235049 :0dccf16
  36be42c0:7ba6da96:1d35149e 20131011135736 :0de1ed9
  58e12d38:0756c7da:0756c7da 20130414235049 :0e15c07
  69e33649:d2b46052:d2b46052 20130422171645 :0e17d4e
  1dd37acb:dcf3e354:dcf3e354 20131011135747 :0eec001
  4b7c50dc:c2bc4887:c2bc4887 20130422171645 :0f0b618
  0f44924c:0f44924c:0f44924c 20130414235049 :0f44924
  1a215d3d:25bd369d:e6d5fe76 20130414235049 :0fb2aba
  30fe4811:431e6ee1:0117adfc 20130524113954 :0ff27f6
  6e73f072:7a97d173:e43858a8 20140328093437 :10502f4
  10ab7036:10ab7036:b7e560e5 20130414235049 :10ab703
  c95cbe14:4cf90d1d:fc10f5f6 20140328093427 :11b4297
  68c7e388:8140b70b:ae096325 20130806174338 :133cff4
  1398b098:1398b098:1398b098 20130414235049 :1398b09
  2bd28388:f2516a22:f2516a22 20130524113952 :139ef92
  95e82eac:0f992270:c877ab64 20131011135735 :144906c
  0de19f82:a4621a87:a4621a87 20130524114003 :1506fc3
  64d30616:13d82a9a:ecc81996 20131203105000 :15260b1
  e9c6b155:014024f1:2e801b15 20131203104912 :152b09a
  7222de21:aaed1bde:40e5c3d0 20130414235049 :15f3494
  975368e0:213d521b:213d521b 20130806174359 :16012d5
  166036ab:166036ab:166036ab 20130414235049 :166036a
  b2275d1c:f7a5eb30:4918803a 20130414235049 :16bbe0c
  6f58c779:11dc44ca:fd83b09e 20131011135735 :171c90f
  68b5039b:0dc5c1a8:4a8bf900 20131203104936 :1728149
  174a4b19:174a4b19:174a4b19 20130414235049 :174a4b1
  97576758:7caa08fd:2f3fb8f8 20131011135720 :179685f
  89258d31:f1bb8ccf:cc515ccd 20130806174331 :17c042b
  97d046c8:9467908f:9467908f 20130806174358 :186e052
  f0dde207:5b731066:5b731066 20130806174343 :1902ce8
  2750162f:ee9e5ec5:ee9e5ec5 20130806174350 :19181db
  95a9e32c:c395f259:925450a6 20130806174335 :1941524
  c3d1820a:d3b3ab0d:d3b3ab0d 20130414235049 :19c0137
  1a6345a2:1a6345a2:1a6345a2 20130414235049 :1a6345a
  5a40b171:9017d436:63e90571 20130414235049 :1ad3be0
  e094b1c1:44ab48c3:5633cb6f 20130414235049 :1b71cda
  b6014f87:f81e1832:f81e1832 20140328093508 :1b7b2d4
  9a4bddf7:40e38844:40e38844 20140328093511 :1c18921
  19335ace:fc1a3d5e:28e1ad96 20130524114001 :1c88458
  bc2ad1bf:94e8eebf:b283b6f7 20140425104156 :1cc110b
  1cee26bc:1cee26bc:1cee26bc 20130414235049 :1cee26b
  401dd13c:3b11d2fc:036ce2ca 20131011135731 :1da3d52
  cd63c0bf:92f964a3:92f964a3 20130524114001 :1daf580
  981f35fd:f48d5b7d:a7d5f82c 20130414235049 :1dedefe
  4bf490fc:4986d4a9:4986d4a9 20140425104152 :1deeabc
  1eb5c9ef:1eb5c9ef:1eb5c9ef 20130414235049 :1eb5c9e
  46084bad:2382a8be:714b157f 20130822143714 :1f18a44
  ee97218b:f3679f41:f3679f41 20130524114006 :1f35cae
  106c63d5:97a86bf6:97a86bf6 20130422171646 :1f4f9e5
  09d3a31a:34a7400a:34a7400a 20130414235049 :1f65630
  202a7fb9:202a7fb9:202a7fb9 20130414235049 :202a7fb
  48a4132f:ebf1fa4f:ebf1fa4f 20130806174356 :2079ca3
  43405316:fb978da1:ed0e2581 20130806174339 :20bc295
  2104ef52:2104ef52:2104ef52 20130414235049 :2104ef5
  34578b7a:f19576cf:f19576cf 20130414235049 :2136ee1
  bac30d9e:3515d95e:633579fc 20130414235049 :216b590
  513d98b0:25b9b371:25b9b371 20140328093509 :21e64d4
  a53af77b:d9198d71:ed143caa 20130414235049 :22863fd
  22fd045b:22fd045b:22fd045b 20130414235049 :22fd045
  232cc1e4:232cc1e4:232cc1e4 20130414235049 :232cc1e
  23cae80c:23cae80c:23cae80c 20130414235049 :23cae80
  cedb6d82:f7cc7817:2362f25c 20130414235049 :242749d
  204ad6d9:7f6eef1b:7f6eef1b 20130524114005 :248a32e
  357b1056:8156e009:8156e009 20130414235049 :24d47d7
  c946fe7e:30421f1a:582cf7c7 20140328093424 :24e0bde
  d7c670b5:f555145a:f555145a 20130806174357 :253c6df
  d3a6da8c:a3784f0b:0d7c7b7a 20130822143714 :25cedd7
  726af6cb:5ad6878a:5ad6878a 20130414235049 :263158a
  265850b3:265850b3:265850b3 20130414235049 :265850b
  def4038f:787984b3:d558718f 20130524114002 :265cb26
  c1327662:79025585:50b28793 20140328093421 :2716120
  bcee12e8:0be27539:0be27539 20140328093525 :279a86b
  0f832edd:81589f14:1651ecce 20131203105140 :27c6f58
  97baa7b5:de42e047:de42e047 20130806174344 :27de591
  f5f5d72d:64b58031:48ecb5fe 20131011135717 :27f8eeb
  eedac93f:52476ec4:effdb45e 20130806174339 :2837db0
  36ef62a5:476a9d0f:773006c0 20130822143714 :2875666
  26250ca7:c150f381:c150f381 20131011135747 :28a6b42
  eff3a295:639027a3:639027a3 20130806174356 :295ba57
  a1e1676a:1399a949:2fece12c 20130806174230 :2a17560
  c716cfad:c357e934:69c529de 20130806174332 :2a26b5e
  7caabb2a:c5a9c9bf:c5a9c9bf 20130819130120 :2a72259
  d9e0bf3a:1d693ab8:60903c8f 20130414235049 :2b318f7
  c92bc1d4:2928de88:ba375fb6 20130524113939 :2bd4340
  84c6ebeb:1dc1193a:1dc1193a 20130806174354 :2bda1f6
  0e158e32:8cdb360f:8cdb360f 20131203105139 :2bde09b
  5c14a520:d1d3073e:45a3b5e7 20130414235049 :2ce2c00
  516ababa:a275e857:a275e857 20130806174342 :2cee6c3
  d3dc14cc:bc3ea362:bc3ea362 20130414235049 :2d33401
  f31b9812:ca52ad89:2f40baca 20130414235049 :2daf8bd
  2dc5d027:2dc5d027:2dc5d027 20130414235049 :2dc5d02
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Comment 1 Curtis Rueden 2014-07-14 12:10:22 CDT 
Sorry for the long delay on replying to this.

Does the behavior still happen with the latest version of Fiji?

Can you create a minimal test case demonstrating the issue? Since you are using a virtual frame buffer, you should be able to reproduce the same behavior on a normal desktop setup, right?