negative z spacing

[W. Chan]

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/)

[Wayne Rasband]

ImageJ does not support negative slice spacing. You should be able to  
work around this problem by removing the minus sign from "Voxel  
Depth" in the Image>Properties dialog box.

-wayne

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/)

[W. Chan]

Thanks Wayne.  It works.

On Thu, 12 Mar 2009, Rasband Wayne wrote:

> ImageJ does not support negative slice spacing. You should be able to work
> around this problem by removing the minus sign from "Voxel Depth" in the
> Image>Properties dialog box.
>
> -wayne
>
> 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/)