ImageJ does not support negative slice spacing. You should be able to
On Mar 12, 2009, at 12:06 AM, W. Chan wrote:
> 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.html>
> I 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/)