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Bug 568 - Cannot measure volume of a layer
Cannot measure volume of a layer
Status: RESOLVED WORKSFORME
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-02-21 19:46 CST by em959089
Modified: 2013-07-07 10:13 CDT
4 users (show)

See Also:
Description em959089 2013-02-21 19:46:47 CST 
[Enter details of the problem or bug and how to reproduce it here.]

Information about your version of Java - this information is useful for the Fiji developers:

  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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\Emily\Desktop\Fiji.app/java/win64/jdk1.6.0_24/jre/
  ij.dir => C:\Users\Emily\Desktop\Fiji.app

Information about the version of each plugin:

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Comment 1 em959089 2013-02-21 19:48:24 CST 
I have an image stack that containes multiple layers and I am able to measure one layer but not another. I set it up to measure and after days it is still measuring.
Comment 2 Curtis Rueden 2013-02-21 20:27:34 CST 
Thanks for the bug report!

It looks like your version of Fiji is not the newest. Can you please run Help > Update Fiji to upgrade to the latest version, then try again?

If it still does not work, can you please comment more specifically what you are trying to do -- what commands you are trying to run, etc.? Otherwise, I'm afraid the problem you're having is not clear enough.

For example, you say, "I am able to measure one layer but not another." Which command(s) are you using to "measure"? Can you record a macro (Plugins > Macros > Record) of the operations you are attempting, and paste it here? Can you upload a sample non-working dataset (if needed) using Help > Upload Sample Image?

(Further reading: http://www.catb.org/esr/faqs/smart-questions.html)
Comment 3 Albert Cardona 2013-02-22 21:44:02 CST 
Dear Emily,

would be instrumental in understanding and resolving the issue that you uploaded in this bug report a minimal test case, for example one of the XML files (no images required) that is giving you the issue, with instructions on which layer can be measured successfully and which cannot.

Thank you.

Albert -- TrakEM2's main author
Comment 4 Johannes Schindelin 2013-07-07 10:13:50 CDT 
We will reopen this issue when the original poster talks to us again ;-)