Re: Cannot use TurboReg plugin by using matlab

Posted by LCY on Dec 10, 2016; 4:46am
URL: http://imagej.273.s1.nabble.com/Cannot-use-TurboReg-plugin-by-using-matlab-tp5017668p5017745.html

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]> 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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> com/Cannot-use-TurboReg-plugin-by-using-matlab-tp5017668p5017679.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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