Re: Is there a mechanism for depth cueing of a stack?

Posted by Joel Sheffield on May 24, 2014; 3:37am
URL: http://imagej.273.s1.nabble.com/Is-there-a-mechanism-for-depth-cueing-of-a-stack-tp5007882p5007898.html

Folks,

Thank you so much for doing this.  As always, I have learned a lot by
reading both of the approaches.  As I understand it, Gabriel's increments
the values along an HSV spectrum, and Curtis directly increments the color
code values --

So far, I've run the macro version, and it seems to be acting as designed.

Again, thank you all.

Joel



Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs


On Fri, May 23, 2014 at 6:37 PM, Gabriel Landini <[hidden email]>wrote:

> On Friday 23 May 2014 22:55:24 Johannes Schindelin wrote:
> > On Fri, 23 May 2014, Gabriel Landini wrote:
> > > I tried Curtis' plugin but I cannot compile it under IJ1.
> >
> > If it does not compile, surely there is some compile error. Could you
> > please paste that into a reply?
>
> Wayne kindly resolved the compilation problem, but now there is another
> issue.
>
>  ImageJ 1.49b9; Java 1.7.0_51 [64-bit]; Linux 3.11.10-11-desktop; 120MB of
> 983MB (12%)
>
> java.lang.NullPointerException
>         at ij3d.ContentCreator.getImages(ContentCreator.java:156)
>         at ij3d.ContentCreator.createContent(ContentCreator.java:63)
>         at ij3d.Image3DUniverse.addContent(Image3DUniverse.java:848)
>         at ij3d.ImageJ3DViewer.add(ImageJ3DViewer.java:137)
>         at Colorized_Rotation.run(Colorized_Rotation.java:39)
>         at ij.plugin.PlugInExecuter.runCompiledPlugin(Compiler.java:324)
>         at ij.plugin.PlugInExecuter.run(Compiler.java:313)
>         at java.lang.Thread.run(Thread.java:744)
>
> I wonder if the 3d viewer version I have in this machine is not the
> expected
> one. I checked the file dates inside the jar in IJ and Fiji and the IJ one
> is
> a bit newer than the Fiji one (11/9/2012 vs 24/5/2012)
>
> > > This macro produces (I hope) the same results.
> >
> > Not quite... Curtis' opens the 3D Viewer and animates the result for
> extra
> > bling.
>
> Oh, well. I said "I hope", since I could not compile it, I could only more
> or
> less guess what it does.
> Below is the macro with the missing bling,although I still do not know if
> it
> does the same thing.
>
> Thanks for looking into this.
> Cheers
>
> Gabriel
>
> ///////////////////////////////
> setBatchMode(true);
> a=getTitle();
> run("RGB Color");
> div=nSlices;
> for(i=0;i<div;i++){
> selectWindow(a);
> setSlice(i+1);
> run("Duplicate...", "title=_b");
> run("HSB Stack");
> setSlice(1);
> run("Set...", "value="+((256/div)*i)+" slice");
> setSlice(2);
> run("Set...", "value=255 slice");
> run("RGB Color");
> imageCalculator("Copy", a ,"_b");
> selectWindow("_b");
> close();
> }
> setBatchMode(false);
> run("3D Viewer");
> call("ij3d.ImageJ3DViewer.setCoordinateSystem", "false");
> call("ij3d.ImageJ3DViewer.add", a, "None", a , "0", "true", "true", "true",
> "2", "0");
> call("ij3d.ImageJ3DViewer.startAnimate");
> ///////////////////////////////
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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