Posted by
Rebecca Keller on
Aug 22, 2014; 9:14pm
URL: http://imagej.273.s1.nabble.com/ABSnake-Error-tp5009311.html
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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