⚠

NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

⚠

NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 1269 - Unexpected behavior of "Pixel units" setting in ImageJ/Fiji Analyze particles
Unexpected behavior of "Pixel units" setting in ImageJ/Fiji Analyze particles
Status: NEW
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2016-05-11 15:06 CDT by Peter J. Lee
Modified: 2016-05-11 15:06 CDT
1 user (show)

See Also:
Description Peter J. Lee 2016-05-11 15:06:05 CDT 
Conditions:
1. Magnification scale is set either manually or from TIFF header.
Procedure:
A. Analyze particles run with "Pixel units" box activated.
B. Analyze particles run with "Pixel units" box deactivated.
Results:
Results tables are the same for both A and B and are scaled using the magnification scale.
Expectation:
When "Pixel units" activated the Results table values would all be in pixels.

Other attempts:
1. Other colleague's Fiji installation (1.51a + java.version => 1.6.0_24)
2. Non-Fiji ImageJ vanilla installation. Image J versions: 1.46, 1.50i, 1.51a (all with same Java version as below).

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.8.0_91
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_91-b14
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.91-b14
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: D:\Data\APPS-O~1\PORTAB~1\FIJI-P~1.APP/..\CommonFiles\Java64
  imagej.dir => D:\Data\APPS-O~1\PORTAB~1\FIJI-P~1.APP

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160504143521)
Fiji: http://update.fiji.sc/ (last check:20160509040721)
Java-8: http://sites.imagej.net/Java-8/ (last check:20160506230031)
2015-Conference: http://sites.imagej.net/2015-Conference/ (last check:20150903130151)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20160401020854)
BAR: http://sites.imagej.net/Tiago/ (last check:20160419120820)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20160510212645)
Biomedgroup: http://sites.imagej.net/Biomedgroup/ (last check:20160318053608)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20160407123326)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20150302170629)
DiameterJ: http://sites.imagej.net/DiameterJ/ (last check:20150923140020)
FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606112449)
Fuzzy logic and artificial neural networks image processing toolbox for ImageJ: http://sites.imagej.net/Astartes91/ (last check:20150906103706)
GDSC: http://sites.imagej.net/GDSC/ (last check:20160510085548)
HDF5: http://sites.imagej.net/Ronneber/ (last check:20150214074119)
IBMP-CNRS: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20150318060643)
IJPB-plugins: http://sites.imagej.net/IJPB-plugins/ (last check:20160502053431)
ImageScience: http://sites.imagej.net/ImageScience/ (last check:20160109083315)
ImagingBook: http://sites.imagej.net/ImagingBook/ (last check:20160429075936)
IMCF Uni Basel: http://sites.imagej.net/UniBas-IMCF/ (last check:20160426093839)
LinearDistance: http://sites.imagej.net/SimonKlein/ (last check:20160323135041)
LOCI: http://sites.imagej.net/LOCI/ (last check:20160219134349)
MiToBo: http://sites.imagej.net/MiToBo/ (last check:20150924081119)
Morphology: http://sites.imagej.net/Landini/ (last check:20160416064441)
MOSAIC ToolSuite: http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last check:20160429073420)
MIST: http://sites.imagej.net/NIST-ISG-MIST/ (last check:20160120135630)
PTBIOP: http://biop.epfl.ch/Fiji-Update/ (last check:20160321084232)
ResultsToExcel: http://sites.imagej.net/ResultsToExcel/ (last check:20151125081931)
Sceptical Physiologist: http://sites.imagej.net/Scepticalphysiologist/ (last check:20151216143531)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20160504110924)
Stowers: http://research.stowers.org/imagejplugins/updates/ (last check:20160510095639)
Fuzzy image processing toolbox for ImageJ: http://sites.imagej.net/Astartes91/ (last check:20150906103706)

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  34af652c (LOCAL_ONLY) 20160418122823 macros/PJL/OlderVersions/LandiniParticles8_AddScaledColumns+GBD and use DAreaEquiv for ROI labels_041816.ijm
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  9248a484 (LOCAL_ONLY) 20160413162549 macros/PJL/OlderVersions/MeasureDequiv+GBD and use Dequiv for ROI labels_041316.txt
  b5d55996 (LOCAL_ONLY) 20160415105351 macros/PJL/OlderVersions/MeasureDequiv+GBD and use Dequiv for ROI labels_041516.ijm
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  047d6239 (LOCAL_ONLY) 20160407143659 macros/PJL/OlderVersions/Rename ROIsetlabels based on their AspectRatios_040716.txt
  bde23746 (LOCAL_ONLY) 20160405123128 macros/PJL/OlderVersions/Rename ROIsetlabels based on their Equiv or Feret Diameter.txt
  e51ad2da (LOCAL_ONLY) 20160406132826 macros/PJL/OlderVersions/Rename ROIsetlabels based on their EquivDiam_040516.txt
  49d95f39 (LOCAL_ONLY) 20160407141132 macros/PJL/OlderVersions/Rename ROIsetlabels based on their EquivDiam_040616.txt
  e3a498e2 (LOCAL_ONLY) 20160407141944 macros/PJL/OlderVersions/Rename ROIsetlabels based on their EquivDiam_040716b.txt
  963de69b (LOCAL_ONLY) 20160408144233 macros/PJL/OlderVersions/Rename ROIsetlabels based on their EquivDiam_040816.txt
  de805867 (LOCAL_ONLY) 20160405125235 macros/PJL/OlderVersions/Rename ROIsetlabels based on their FeretDiam_040516.txt
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  13dd3014 (LOCAL_ONLY) 20160413163231 macros/PJL/OlderVersions/Rename ROIsetlabels with AspectRatios_041316.txt
  69170700 (LOCAL_ONLY) 20160413154637 macros/PJL/OlderVersions/Rename ROIsetlabels with FeretDiams_041316.txt
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