problem with conversion to RGB - IJ 1.51k18 java 1.6.0_20

Posted by Cammer, Michael on Feb 24, 2017; 9:26pm
URL: http://imagej.273.s1.nabble.com/problem-with-conversion-to-RGB-IJ-1-51k18-java-1-6-0-20-tp5018189.html

We are having a problem converting hyperstacks to RGB in a macro.  Approximately one out of five times we run the macro, it does not work.  We tried adding a wait(200) step, but don't know if this really helps or not.

The error is that ImageJ cannot find image with id2.

[cid:[e-mail]7A15E0]

Any help appreciated.  The problem is with the second macro.  Included the first macro to show what types of files we are using (2 or 3 channel Z series confocal).

macro "Set up images [q]" {
  //run("Channels Tool...");
  Stack.setDisplayMode("composite");
  //run("Brightness/Contrast...");
  Stack.getDimensions(width, height, channels, slices, frames) ;
  for (n=1; n<=channels; n++) {
    Stack.setChannel(n);
    setMinAndMax(0, 65535);
  }
  Stack.setSlice(floor(slices / 3)) ;
}

/*  Draw a box around an area to be 3D projected.
     Run this macro.
*/
macro "Do 3D projections [F2]" {
   run("Duplicate...", "duplicate");
   id1 = getImageID();
   // change to get scale for each sample if Z different than 0.3 um
   run("3D Project...", "projection=[Brightest Point] axis=X-Axis slice=0.30 initial=0 total=360 rotation=10 lower=1 upper=255 opacity=0 surface=50 interior=25 interpolate");
   //run("RGB Color", "frames");  // buggy
   wait(200);   // appears the projection command needs this to hand off the image properly
   id2 = getImageID();
   run("RGB Color", "frames keep");
   selectImage(id1); close(); selectImage(id2); close();
}








=*===========================================================*=
Michael Cammer, DART Microscopy Laboratory, NYU Langone Medical Center
    Cell:  914-309-3270     Office: Skirball 2nd Floor main office, back right
      http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/


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