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Stitching exception

zhaoliang
Hi all,

I meet a problem when stitching images in Fiji.

1. One exception happened when Fiji is loading one of images in the plugin Grid/collection stitching, which is:

The Log says QuickTime for Java is not supported with a 64-bit JVM. Please invoke the 32-bit(-d32 to utilize QTjava function).

So I change this image type to 32-bit. And it work then. But I am not sure whether it is right solution?

2. when fuse and display, and exception occurred below:

(Fiji Is Just) ImageJ 2.0.0-rc-59/1.51j; Java 1.8.0_66 [64-bit]; Linux 3.10.0-327.36.3.el7.x86_64; 12623MB of 142550MB (8%)
 
java.lang.NegativeArraySizeException
        at ij.process.FloatProcessor.<init>(FloatProcessor.java:37)
        at net.imglib2.img.imageplus.FloatImagePlus.<init>(FloatImagePlus.java:69)
        at net.imglib2.img.imageplus.ImagePlusImgFactory.createFloatInstance(ImagePlusImgFactory.java:114)
        at net.imglib2.type.numeric.real.FloatType.createSuitableNativeImg(FloatType.java:90)
        at net.imglib2.img.imageplus.ImagePlusImgFactory.create(ImagePlusImgFactory.java:69)
        at net.imglib2.img.imageplus.ImagePlusImgFactory.create(ImagePlusImgFactory.java:64)
        at net.imglib2.img.ImgFactory.create(ImgFactory.java:84)
        at mpicbg.stitching.fusion.Fusion.fuse(Fusion.java:105)
        at plugin.Stitching_Grid.run(Stitching_Grid.java:599)
        at ij.IJ.runUserPlugIn(IJ.java:217)
        at ij.IJ.runPlugIn(IJ.java:181)
        at ij.Executer.runCommand(Executer.java:137)
        at ij.Executer.run(Executer.java:66)
        at java.lang.Thread.run(Thread.java:745)

I am so confused and do not know how to solve it. Any suggestions please?

Best,
Allen
 

 
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Re: Stitching exception

Stephan.Preibisch@mdc-berlin.de
Hi Allen,

this happens because your image is bigger than 2^31 pixels in the xy plane, which is currently not supported by the standard ImageJ. You could use TrakEM2 for Stitching, but we are also developing Stitching based on ImgLib2 which does not have these limitations. It will still take a little though...

The QTjava is not required, so it is better to use the 64bit JVM.

Hope this helps,
Stephan
---

Dr. Stephan Preibisch
Group Leader

Berlin Institute of Medical Systems Biology of the MDC
Building 89, 1.08b

email: [hidden email]<mailto:[hidden email]>
web: http://preibischlab.mdc-berlin.de

On 5 Mar 2017, at 22:41, zhaoliang <[hidden email]<mailto:[hidden email]>> wrote:

Hi all,

I meet a problem when stitching images in Fiji.

1. One exception happened when Fiji is loading one of images in the plugin
Grid/collection stitching, which is:

The Log says QuickTime for Java is not supported with a 64-bit JVM. Please
invoke the 32-bit(-d32 to utilize QTjava function).

So I change this image type to 32-bit. And it work then. But I am not sure
whether it is right solution?

2. when fuse and display, and exception occurred below:

(Fiji Is Just) ImageJ 2.0.0-rc-59/1.51j; Java 1.8.0_66 [64-bit]; Linux
3.10.0-327.36.3.el7.x86_64; 12623MB of 142550MB (8%)

java.lang.NegativeArraySizeException
at ij.process.FloatProcessor.<init>(FloatProcessor.java:37)
at net.imglib2.img.imageplus.FloatImagePlus.<init>(FloatImagePlus.java:69)
at
net.imglib2.img.imageplus.ImagePlusImgFactory.createFloatInstance(ImagePlusImgFactory.java:114)
at
net.imglib2.type.numeric.real.FloatType.createSuitableNativeImg(FloatType.java:90)
at
net.imglib2.img.imageplus.ImagePlusImgFactory.create(ImagePlusImgFactory.java:69)
at
net.imglib2.img.imageplus.ImagePlusImgFactory.create(ImagePlusImgFactory.java:64)
at net.imglib2.img.ImgFactory.create(ImgFactory.java:84)
at mpicbg.stitching.fusion.Fusion.fuse(Fusion.java:105)
at plugin.Stitching_Grid.run(Stitching_Grid.java:599)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)

I am so confused and do not know how to solve it. Any suggestions please?

Best,
Allen






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Re: Stitching exception

zhaoliang
Hi Stephan,

Many thanks for your help. That's quite helpful and save me much time.

One thing I am still confused is 'fuse and display' by stitching plugin. Fi=
ji sometimes can not show me the final combined image but just show Fusing =
time point: 1 of 1...  even after 8 hours waiting.

Is it the problem of the too large quantity numbers of the images that Fiji=
 cannot display the result or anything else? How can I improve it?

Best,

Allen
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