Fiji: color deconvolution macro

Posted by Rodrigo Gonçalves on Apr 08, 2015; 2:54pm
URL: http://imagej.273.s1.nabble.com/Fiji-color-deconvolution-macro-tp5012404.html

Dear all,

I'm preparing a macro in Fiji to run color deconvolution in all images inside a given folder (using Process-Batch-Macro).
What I intend is, for each image:- Run color deconvolution with my user-defined colour vectors
- Save the first resulting image (colour 1) as a TIFF file in the same folder
I recorded the macro while doing color deconvolution and I can assign my user-defined values to the vectors. However the macro runs without showing the results.

The log file seems ok and there are no error messages or anything, but doesn't show anything else than the log.
I copy here the macro (and the log further down).
What am I missing?Thanks!Rodrigo

---- start of macro code ---// Colour vectors to use:

//Colour[1]:

  Red1=13.951654
  Green1=23.660986
  Blue1=19.173325
 
//Colour[2]:

  Red2=7.737847
  Green2=7.301559
  Blue2=9.771005
 
//Colour[3]:

  Red3=144.38943
  Green3=112.913376
  Blue3=85.59621


run("Colour Deconvolution", "vectors=[User values] show [r1]=Red1 [g1]=Green1 [b1]=Blue1 [r2]=Red2 [g2]=Green2 [b2]=Blue2 [r3]=Red3 [g3]=Green3 [b3]=Blue3");
---- end of macro code ---

---- start of log text ---User values Vector Matrix ---
Colour[1]:
  R1: 13.951654
  G1: 23.660986
  B1: 19.173325
 
Colour[2]:
  R2: 7.737847
  G2: 7.301559
  B2: 9.771005
 
Colour[3]:
  R3: 144.38943
  G3: 112.913376
  B3: 85.59621
 
User values Java code ---
        if (myStain.equals("New_Stain")){
        // This is the New_Stain
            MODx[0]=0.41649377;
            MODy[0]=0.706343;
            MODz[0]=0.57237446;
            MODx[1]=0.5356745;
            MODy[1]=0.5054712;
            MODz[1]=0.67642564;
            MODx[2]=0.7137465;
            MODy[2]=0.5581539;
            MODz[2]=0.42311957;
}
---- end of log text ---

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