Posted by
W. Chan on
Mar 12, 2009; 4:06am
URL: http://imagej.273.s1.nabble.com/negative-z-spacing-tp3693317.html
Hi
I have some z stacks with a negative Z spacing and when I did a Image |
Stacks | Reslice ..., I got an exception (1.42h, java 1.6.0_12 on win xp
sp3).
java.lang.NullPointerException
at ij.ImagePlus.setStack(ImagePlus.java:509)
at ij.ImagePlus.<init>(ImagePlus.java:144)
at ij.plugin.Slicer.resliceRectOrLine(Slicer.java:298)
at ij.plugin.Slicer.reslice(Slicer.java:100)
at ij.plugin.Slicer.run(Slicer.java:70)
at ij.IJ.runPlugIn(IJ.java:149)
at ij.Executer.runCommand(Executer.java:119)
at ij.Executer.run(Executer.java:58)
at java.lang.Thread.run(Unknown Source)
I can eliminate the error by either removing the negative sign for both
input and output Z spacing, or select avoid interpolation (but will mess
up the aspect ratio). However, in the daily build 1.42k, there is only a
single entry for slice spacing. When I left the negative sign in place, I
got a nullpointer exception as above. When I removed the negative sign, I
got another error.
java.lang.NegativeArraySizeException
at
ij.process.ByteProcessor.createProcessor(ByteProcessor.java:117)
at ij.process.ByteProcessor.resize(ByteProcessor.java:893)
at ij.plugin.Slicer.getSlice(Slicer.java:355)
at ij.plugin.Slicer.resliceRectOrLine(Slicer.java:290)
at ij.plugin.Slicer.reslice(Slicer.java:101)
at ij.plugin.Slicer.run(Slicer.java:71)
at ij.IJ.runPlugIn(IJ.java:150)
at ij.Executer.runCommand(Executer.java:119)
at ij.Executer.run(Executer.java:58)
at java.lang.Thread.run(Unknown Source)
How do I go about fixing this?
I obtained z stacks on 2 BioRad confocals using either CoMOS or LaserSharp
2000. In both software, the slices are arranged in the order they are
acquired and not by the axial position. Positive direction is defined
as going into the sample. If I acquire the bottom slice first, I will get
a negative slice spacing and an inverted stack with respect to the actual
Z-position. You can see an example here.
http://staff.washington.edu/wpchan/mrc/zstack.htmlI can use Bob Dougherty's stack sorter to reverse the stack but it still
has the negative Z spacing that can cause reslice to choke. I wonder how
other software packages operate in similar situation. Do they generate a
negative z spacing? Thanks for any advice.
--
Pang (Wai Pang Chan,
[hidden email], PAB A087, 206-685-1519)
The Biology Imaging Facility (
http://staff.washington.edu/wpchan/if/)