http://imagej.273.s1.nabble.com/Cannot-use-TurboReg-plugin-by-using-matlab-tp5017668p5017746.html
have two windows "stack1.tif" and "AVG_stack1.tif". See TurboReg
> Hi Yuekan,
>
> Thank you very much for your help. Maybe you are right. However, I don't
> know how to specify the source and target from ' -file ' to ' -window '.
> Could you please show me an example?
>
> All the best,
>
> Chunyue
>
> 2016-12-06 0:40 GMT+08:00 Yuekan Jiao-2 [via ImageJ] <
>
[hidden email]>:
>
> > Hi Chunyue,
> >
> > If I understand, you have 2 opened windows "stack1.tif" and
> > "AVG_stack1.tif", you need to specify the source and target from ' -file
> > '
> > to ' -window '. file paths do not matter.
> >
> > I am not sure that TurboReg can do alignment for a stack, but a single
> > slice should be fine.
> >
> > Yuekan
> >
> > On Fri, Dec 2, 2016 at 11:49 PM, LCY <[hidden email]
> > <
http:///user/SendEmail.jtp?type=node&node=5017688&i=0>> wrote:
> >
> > > Hi Curtis,
> > >
> > > Thank you very much for your help!
> > >
> > > This is what I have: window 10 system, Matlab 2015b, Fiji(based on java
> > 6)
> > > which I store in "C:\Users\[my name]\Fiji.app".
> > >
> > > I want to do matching among many tiff stacks. Because my other codes
> are
> > > programmed by Matlab, I want to use TurboReg plugin from Matlab to
> > process
> > > these files automatically.
> > >
> > > *This is how I do that* :
> > > step 1: update Fiji as you suggested;
> > > step 2: add path in Matlab:"C:\Users\[my name]\Fiji.app\scripts"
> > > step 3: start Fiji in my Matlab code by using the command "Miji;"
> > > step 4: open one tiff stack file by using "MIJ.run('Open...',
> > > ['path=','F:\TwoPhotonfile\stack1.tif']);"
> > > step 5: normalize and average my tiff stack file by using
> > > MIJ.run('Open...',...) and MIJ.run('Enhance Contrast...',..)
> > separately.
> > > step 6: now there are two opened windows, one is the normalized tiff
> > stack
> > > file, the other is the averaged image file (contains only one image)
> > > step 7: do matching by using
> > > " MIJ.run('TurboReg ', ['-align ', '-file ','stack1.tif',' ','0 0
> > > ',num2str(width),' ',num2str(height),' ',...
> > > '-file ','AVG_stack1.tif',' ','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']); "
> > >
> > > *The results showed in ImageJ Exception are as follow:*
> > > "ImageJ 1.50e; Java 1.7.0_60 [64-bit]; Windows 8 6.2; 178MB of 3725MB
> > (4%)
> > >
> > > java.lang.NullPointerException
> > > at TurboReg_.alignImages(TurboReg_.java:893)
> > > at TurboReg_.run(TurboReg_.java:636)
> > > at ij.IJ.runUserPlugIn(IJ.java:212)
> > > at ij.IJ.runPlugIn(IJ.java:176)
> > > at ij.Executer.runCommand(Executer.java:136)
> > > at ij.Executer.run(Executer.java:65)
> > > at ij.IJ.run(IJ.java:292)
> > > at MIJ.run(MIJ.java:1171)"
> > >
> > > *This is what I have done:*
> > >
> > > I try to change the source path to 'F:\TwoPhotonfile\stack1.tif', but
> > this
> > > doesn' t work;
> > > I double clicked the information in Exception window, it showed "file
> is
> > > not
> > > in a supported format, a reader plugin is not available, or it was not
> > > found". But, this plugin works when I use it manually.
> > >
> > > Thank you for your help, Curtis!
> > >
> > > All the best,
> > >
> > > Chunyue
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > --
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> > >
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