Problem with 3D Object Counter

[Devivier C.]

Dear All,

I am trying to use 3D object counter to obtain an information about the volume and spatial distributions of particles. The volume is 1894x1894x1586 coded in unsigned 16 bits. I have attached the parameters that I used to run the command. Below is the error that I have.

(Fiji Is Just) ImageJ 2.0.0-rc-47/1.50g; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 16539MB of 147306MB (11%)
java.lang.ArrayIndexOutOfBoundsException: 1394389000
     at Utilities.Counter3D.imgArrayModifier(Counter3D.java:652)
     at Utilities.Counter3D.<init>(Counter3D.java:88)
     at _3D_objects_counter.run(_3D_objects_counter.java:186)
     at ij.IJ.runUserPlugIn(IJ.java:212)
     at ij.IJ.runPlugIn(IJ.java:176)
     at ij.Executer.runCommand(Executer.java:137)
     at ij.Executer.run(Executer.java:66)
     at java.lang.Thread.run(Thread.java:745)

What have I done wrong?

Thank you for your help,
Cédric

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[Thomas Boudier-4]

Hi Cédric,

Looks like your image is very very big ;) . I think OC uses a 1D array
to store the data, this is why it crashed. Try the implementation in the
3D ImageJ suite :

http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:3d_spots_segmentation:start 
, then plugins/3D/simple segmentation provided you have a lot of RAM...

Best,

Thomas


On 12/04/2016 19:51, Devivier C. wrote:

> Dear All,
>
> I am trying to use 3D object counter to obtain an information about the volume and spatial distributions of particles. The volume is 1894x1894x1586 coded in unsigned 16 bits. I have attached the parameters that I used to run the command. Below is the error that I have.
>
> (Fiji Is Just) ImageJ 2.0.0-rc-47/1.50g; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 16539MB of 147306MB (11%)
> java.lang.ArrayIndexOutOfBoundsException: 1394389000
>       at Utilities.Counter3D.imgArrayModifier(Counter3D.java:652)
>       at Utilities.Counter3D.<init>(Counter3D.java:88)
>       at _3D_objects_counter.run(_3D_objects_counter.java:186)
>       at ij.IJ.runUserPlugIn(IJ.java:212)
>       at ij.IJ.runPlugIn(IJ.java:176)
>       at ij.Executer.runCommand(Executer.java:137)
>       at ij.Executer.run(Executer.java:66)
>       at java.lang.Thread.run(Thread.java:745)
>
> What have I done wrong?
>
> Thank you for your help,
> Cédric
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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  /***************************************************************/
       Thomas Boudier, Associate Professor, UPMC,
       Université Pierre et Marie Curie, Paris, France.
       BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/

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