Re: Cannot use TurboReg plugin by using matlab

Posted by ctrueden on Dec 02, 2016; 12:16pm
URL: http://imagej.273.s1.nabble.com/Cannot-use-TurboReg-plugin-by-using-matlab-tp5017668p5017674.html

Hi Chunyue,

Download a Life-Line version of Fiji and update it to the latest version.
This will give you a Java 6 compatible version of Fiji, which you can use
with MATLAB.

See:
http://imagej.net/2016-05-10_-_ImageJ_HOWTO_-_Java_8,_Java_6,_Java_3D

I would not recommend trying to compile individual components to use Java
7—you will have many problems.

Alternately, as Mario said, you can try updating MATLAB to use Java 8.

Hopefully Mathworks will update MATLAB to support Java 8 in the future.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
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On Thu, Dec 1, 2016 at 7:28 PM, LCY <[hidden email]> wrote:

> Hi, Mario,
>
> Thank you very much for your help! Maybe I can try other plugins that have
> the same function with TurboReg.
>
> All the best,
>
> Chunyue
>
>
>
> 2016-12-01 22:14 GMT+08:00 Mario Emmenlauer-3 [via ImageJ] <
> [hidden email]>:
>
> > Hi Chunyue,
> >
> > On 01.12.2016 14:43, LCY wrote:
> >
> > > Dear all,
> > >
> > > I try to align a tiff stack to a tiff template image.  The tiff stack
> > > contains more than 900 images, so I write a  Matlab code to use
> TurboReg
> > to
> > > finish this step. The code is as follow:
> > >
> > > MIJ.run('TurboReg ', ['-align ', '-file ',fileNames{1,1},' ','0 0 ',
> > > num2str(width),' ',num2str(height),' ',
> > >     '-file ',fileNames{2,1},' ','0 0 ',num2str(width),' ',
> > num2str(height)
> > > ,' ','-rigidBody ',num2str(width/2),' ',num2str(height/2),'
> > > ',num2str(width/2),' ',num2str(height/2),' ','0',num2str(height/2),'
> > ','0
> > > ',num2str(height/2),' ',num2str(width-1),' ',num2str(height/2),'
> > > ',num2str(width-1),' ',num2str(height/2),' ','-showOutput']);
> > >
> > > However, ImageJ Exception showed as follow:
> > > " ImageJ 1.51h; Java 1.7.0_60 [64-bit]; Windows 8 6.2; 422MB of 3725MB
> > (11%)
> > >
> > > java.lang.UnsupportedClassVersionError: HandleExtraFileTypes :
> > Unsupported
> > > major.minor version 52.0
> > >
> > > This plugin requires Java 1.8 or later."
> > >
> > > Fiji outside Matlab showed java' version is 1.8.0_112. But when I
> > launched
> > > ImageJ from Matlab, the java version changed to  1.7.0_60.
> >
> > Matlab brings its own version of Java. Its an integral part of
> > Matlab. I can not recommend running Matlab with a different version
> > of Java, and certainly not going from 1.7 to 1.8 (unless somebody
> > has by chance good experience with this). I tried it in the past and
> > got many problems.
> >
> > It might be a lot easier to compile your Fiji dependencies with
> > Java 1.7 and use this in Matlab.
> >
> > Hope this helps...
> >
> > Viele Grüße,
> >
> >     Mario Emmenlauer
> >
> >
> > --
> > BioDataAnalysis GmbH, Mario Emmenlauer      Tel. Buero: [phone]
> > <+49%2089%2074677203>
> > Balanstr. 43                   mailto: memmenlauer * biodataanalysis.de
> > D-81669 München                          http://www.biodataanalysis.de/
> >
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