ABSnake Error

[Rebecca Keller]

In trying to segment/track my cells using the ABSnake plugin, I get the
error posted below. OS is 64bit Win7, 32GB memory, and my image stack is a
16-bit .lsm confocal timelapse in one color/channel only (2D+t), opened by
the non-SCIFIO option. I get the same results if I convert to 8-bit first.
Seems like it can't open the second image for some reason.

Options used in plugin were all the defaults, except I ticked "create seg
image." Tried it without that option also, similar results. Also tried with
a single ROI instead of 16, to no avail. ROIs were created by thresholding
then magic wand.

Also, image is reported as "locked' after this error, which I've never
encountered. I have to restart the whole process to tinker with it.

Tried to give all necessary info, please forgive if I've forgotten
something.

JPK


Log:

processing slice 1 with roi 0
processing slice 1 with roi 1
processing slice 1 with roi 2
processing slice 1 with roi 3
processing slice 1 with roi 4
processing slice 1 with roi 5
processing slice 1 with roi 6
processing slice 1 with roi 7
processing slice 1 with roi 8
processing slice 1 with roi 9
processing slice 1 with roi 10
processing slice 1 with roi 11
processing slice 1 with roi 12
processing slice 1 with roi 13
processing slice 1 with roi 14
processing slice 1 with roi 15


Error Message:

(Fiji Is Just) ImageJ 2.0.0-rc-14/1.49f; Java 1.6.0_24 [64-bit]; Windows 7
6.1; 1869MB of 24465MB (7%)

java.lang.NegativeArraySizeException
at ij.gui.PolygonRoi.<init>(PolygonRoi.java:39)
at ABSnake.createRoi(ABSnake.java:216)
at ABSnake_.run(ABSnake_.java:211)
at
ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262)
at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:111)
at ij.IJ.runUserPlugIn(IJ.java:204)
at ij.IJ.runPlugIn(IJ.java:166)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)

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[Thomas Boudier]

Hi,

The usual error comes from the initialization, you can try using
"Edit/Selection/Fit spline" for your ROIs.

Best,

Thomas

Le 22/08/2014 23:16, Rebecca Keller a écrit :

> In trying to segment/track my cells using the ABSnake plugin, I get the
> error posted below. OS is 64bit Win7, 32GB memory, and my image stack is a
> 16-bit .lsm confocal timelapse in one color/channel only (2D+t), opened by
> the non-SCIFIO option. I get the same results if I convert to 8-bit first.
> Seems like it can't open the second image for some reason.
>
> Options used in plugin were all the defaults, except I ticked "create seg
> image." Tried it without that option also, similar results. Also tried with
> a single ROI instead of 16, to no avail. ROIs were created by thresholding
> then magic wand.
>
> Also, image is reported as "locked' after this error, which I've never
> encountered. I have to restart the whole process to tinker with it.
>
> Tried to give all necessary info, please forgive if I've forgotten
> something.
>
> JPK
>
>
> Log:
>
> processing slice 1 with roi 0
> processing slice 1 with roi 1
> processing slice 1 with roi 2
> processing slice 1 with roi 3
> processing slice 1 with roi 4
> processing slice 1 with roi 5
> processing slice 1 with roi 6
> processing slice 1 with roi 7
> processing slice 1 with roi 8
> processing slice 1 with roi 9
> processing slice 1 with roi 10
> processing slice 1 with roi 11
> processing slice 1 with roi 12
> processing slice 1 with roi 13
> processing slice 1 with roi 14
> processing slice 1 with roi 15
>
>
> Error Message:
>
> (Fiji Is Just) ImageJ 2.0.0-rc-14/1.49f; Java 1.6.0_24 [64-bit]; Windows 7
> 6.1; 1869MB of 24465MB (7%)
>
> java.lang.NegativeArraySizeException
> at ij.gui.PolygonRoi.<init>(PolygonRoi.java:39)
> at ABSnake.createRoi(ABSnake.java:216)
> at ABSnake_.run(ABSnake_.java:211)
> at
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:262)
> at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:111)
> at ij.IJ.runUserPlugIn(IJ.java:204)
> at ij.IJ.runPlugIn(IJ.java:166)
> at ij.Executer.runCommand(Executer.java:131)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:662)
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

--
  /**********************************************************/
     Thomas Boudier, MCU Université Pierre et Marie Curie,
     Modélisation Cellulaire et Imagerie Biologique (EE1),
     IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu.
     Tel : [phone]   Fax : [phone]
/*******************************************************/

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[rachelgomez123]

It sounds like you're encountering an error while trying to use a plugin with an image stack. The error message you provided suggests that there is an issue with opening the second image in the stack.

There could be a few possible reasons for this error:

The image stack file may be corrupted or incomplete, causing an issue when trying to open the second image. You could try re-exporting the image stack file or opening it with a different program to see if it loads correctly.

The plugin may not be compatible with your version of ImageJ or the file format of the image stack. You could try updating ImageJ to the latest version or contacting the plugin developer for support.

There may not be enough memory available to load the entire image stack into memory. You mentioned that you have 32GB of memory, which should be sufficient for most image stacks, but it's possible that other programs or processes are using a significant amount of memory, leaving less available for ImageJ. You could try closing other programs or processes and restarting ImageJ to free up memory.


Regards,
Rachel Gomez