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Bug 326 - Simple Neurite Tracer
Simple Neurite Tracer
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2011-06-21 13:28 CDT by Katrin Janz
Modified: 2011-06-24 19:11 CDT
1 user (show)

See Also:
Description Katrin Janz 2011-06-21 13:28:51 CDT 
Hello everyone,  I'm currently working with the plugin Simple Neurite Tracer and I'm having the following problem. After opening the file and activating Hessian-based analysis the program is not able to find the right trace along the axon. Their are two possible outcomes, a path next to the axon or a path which is totally out of target. Even without activating the Hessian-based analysis this problem occurs. The files I use are normal lsm.files. 
So maybe you can help, thanks a lot. 

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

  os.arch => x86
  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) Client 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: Up-to-date

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: \\fp0.uni-kl.de\DFS\tu\bio\tierphys\Benutzer\kjanz\Desktop\FIJI-W~1\Fiji.app/java/win32/jdk1.6.0_24/jre
  fiji.dir => \\fp0.uni-kl.de\DFS\tu\bio\tierphys\Benutzer\kjanz\Desktop\FIJI-W~1\Fiji.app

Information about the version of each plugin:

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Comment 1 Mark Longair 2011-06-22 11:10:14 CDT 
Thanks for reporting this problem.  I can't reproduce this with the files that I have here, though, and there might be a number of different things going wrong.  Would it be possible for you to upload an example file that you see this problem with?  You should be able to do that with the "Help > Upload Sample Image" in Fiji, or (if the file's not too large) you can email it to: mark-imagej at longair dot net
Comment 2 Katrin Janz 2011-06-22 12:52:32 CDT 
(In reply to comment #1)
> Thanks for reporting this problem.  I can't reproduce this with the files that
> I have here, though, and there might be a number of different things going
> wrong.  Would it be possible for you to upload an example file that you see
> this problem with?  You should be able to do that with the "Help > Upload
> Sample Image" in Fiji, or (if the file's not too large) you can email it to:
> mark-imagej at longair dot net
> 

I uploaded the file I have the problems with, it's called 110412_E2_LSO_40x.
Comment 3 Mark Longair 2011-06-24 18:04:50 CDT 
Katrin,

Thank you for uploading that file, and sorry about my delay in replying - this has been a very busy week for me.

I think the problem is the unusual calibration values set in your file.  The z spacing is set to 0.75 micrometres, but the x and y spacing are both set to 1.0E-13 micrometres.  The latter two must be wrong, and Simple Neurite Tracer can only work properly when these values are correct.  If you know the correct values, it's probably best to set them for each file using "Image > Properties ..." and save out each file in a new directory.  (Simple Neurite Tracer only reads the calibration values when it starts up, so if you're just testing and have made such changes, you will need to quit the tracer and start it again before retrying.)

I hope that's of some help.

best regards,
mark
Comment 4 Katrin Janz 2011-06-24 18:16:10 CDT 
(In reply to comment #3)
> Katrin,
> 
> Thank you for uploading that file, and sorry about my delay in replying - this
> has been a very busy week for me.
> 
> I think the problem is the unusual calibration values set in your file.  The z
> spacing is set to 0.75 micrometres, but the x and y spacing are both set to
> 1.0E-13 micrometres.  The latter two must be wrong, and Simple Neurite Tracer
> can only work properly when these values are correct.  If you know the correct
> values, it's probably best to set them for each file using "Image > Properties
> ..." and save out each file in a new directory.  (Simple Neurite Tracer only
> reads the calibration values when it starts up, so if you're just testing and
> have made such changes, you will need to quit the tracer and start it again
> before retrying.)
> 
> I hope that's of some help.
> 
> best regards,
> mark
> 

Thank you so so very much! That will fix my problem! You did a really great job inventing this tool, makes my work a lot easier, so thanks!
Regards Katrin
Comment 5 Mark Longair 2011-06-24 19:11:11 CDT 
Great, I'm glad to hear that's sorted out, and thanks for your kind remarks.  I'm closing the bug with this comment.

best regards,
mark