/*
Macros for ImageJ 1.51t by Michael Cammer  mcammer@gmail.com  http://microscopynotes.com/  
If you use these macros, please acknowledge the DART Microscopy Core Laboratory at NYU Health.
v100 20171214


*/


macro "Color using max" {
  original = getImageID;
  t = getTitle;
  run("Z Project...", "stop=6 projection=[Max Intensity]");
  rename("b");
  run("Enhance Contrast...", "saturated=0 normalize");
  selectImage(original);
  run("Z Project...", "start=8 stop=11 projection=[Max Intensity]");
  run("Enhance Contrast...", "saturated=0 normalize");
  rename("g");
  selectImage(original);
  run("Z Project...", "start=13 projection=[Max Intensity]");
  run("Enhance Contrast...", "saturated=0 normalize"); 
  rename("r");
  run("Merge Channels...", "c1=r c2=g c3=b create");
  rename("maxmerged_" + t);
}

macro "Color using avg" {
  original = getImageID;
  t = getTitle;
  run("Z Project...", "stop=6 projection=[Average Intensity]");
  rename("b");
//  run("Enhance Contrast...", "saturated=0 normalize");
  selectImage(original);
  run("Z Project...", "start=8 stop=11 projection=[Average Intensity]");
//  run("Enhance Contrast...", "saturated=0 normalize");
  rename("g");
  selectImage(original);
  run("Z Project...", "start=13 projection=[Average Intensity]");
//  run("Enhance Contrast...", "saturated=0 normalize"); 
  rename("r");
  run("Merge Channels...", "c1=r c2=g c3=b create");
  rename("avgmerged_" + t);
  run("RGB Color");
  run("Scale Bar...", "width=10 height=5 font=18 color=Gray background=None location=[Lower Left] bold");
}


macro "simple graph intrensity by wavelength range" {
  run("Hyperstack to Stack");
  run("Plot Z-axis Profile");
}

macro "extract two channels and remerge" {
  original = getImageID;
  t = getTitle;
  b = "blue"+t;
  r  = "red" + t;
  run("Duplicate...", "title=["+b+"] duplicate channels=10");
  selectImage(original);
  run("Duplicate...", "title=["+r+"] duplicate channels=20");
  run("Merge Channels...", "c1=[" + r + "] c3=["+b+"] create");
  rename("ch10and20_"+t);

}


macro "extract two channels and remerge MC" {
  original = getImageID;
  t = getTitle;
  b = "blue"+t;
  r  = "red" + t;
  run("Duplicate...", "title=["+b+"] duplicate channels=10");
  selectImage(original);
  run("Duplicate...", "title=["+r+"] duplicate channels=20");
  run("Merge Channels...", "c7=[" + r + "] c5=["+b+"] create");
  rename("ch10and20_"+t);

}



macro "Plot spectrum"  {
  t = getTitle;
  start = 415;  // approx average of 409.92320200000012-418.82141700000017
  step = 9;       // nm
  run("Hyperstack to Stack");
  slices = nSlices;
  run("Set Measurements...", "mean redirect=None decimal=3");
  run("Clear Results");
  for(s=1; s<=slices; s++) {
   setSlice(s);
   run("Measure");
  }
  nmlabels = newArray(nResults);
  intensities = newArray(nResults);
  for (i=0; i<nResults; i++) {
    intensities[i] = getResult("Mean", i);
    nmlabels[i] = start + (i*step);
  }
    

  Plot.create(t, "nm", "intensity (a.u.)", nmlabels, intensities);

}




/*
Information|Image|Channel|DetectionWavelength|Ranges #01 = 409.92320200000012-418.82141700000017
Information|Image|Channel|DetectionWavelength|Ranges #02 = 418.82141700000017-427.71963200000016
Information|Image|Channel|DetectionWavelength|Ranges #03 = 427.71963200000016-436.61784700000021
Information|Image|Channel|DetectionWavelength|Ranges #04 = 436.61784700000021-445.5160620000002
Information|Image|Channel|DetectionWavelength|Ranges #05 = 445.5160620000002-454.4142770000002
Information|Image|Channel|DetectionWavelength|Ranges #06 = 454.4142770000002-463.31249200000025
Information|Image|Channel|DetectionWavelength|Ranges #07 = 463.31249200000025-472.21070700000024
Information|Image|Channel|DetectionWavelength|Ranges #08 = 472.21070700000024-481.10892200000023
Information|Image|Channel|DetectionWavelength|Ranges #09 = 481.10892200000023-490.00713700000023
Information|Image|Channel|DetectionWavelength|Ranges #10 = 490.00713700000023-498.90535200000028
Information|Image|Channel|DetectionWavelength|Ranges #11 = 498.90535200000028-507.80356700000027
Information|Image|Channel|DetectionWavelength|Ranges #12 = 507.80356700000027-516.70178200000032
Information|Image|Channel|DetectionWavelength|Ranges #13 = 516.70178200000032-525.59999700000026
Information|Image|Channel|DetectionWavelength|Ranges #14 = 525.59999700000026-534.49821200000031
Information|Image|Channel|DetectionWavelength|Ranges #15 = 534.49821200000031-543.39642700000036
Information|Image|Channel|DetectionWavelength|Ranges #16 = 543.39642700000036-552.29464200000041
Information|Image|Channel|DetectionWavelength|Ranges #17 = 552.29464200000041-561.19285700000034
Information|Image|Channel|DetectionWavelength|Ranges #18 = 561.19285700000034-570.09107200000039
Information|Image|Channel|DetectionWavelength|Ranges #19 = 570.09107200000039-578.98928700000045
Information|Image|Channel|DetectionWavelength|Ranges #20 = 578.98928700000045-587.88750200000038
Information|Image|Channel|DetectionWavelength|Ranges #21 = 587.88750200000038-596.78571700000043
Information|Image|Channel|DetectionWavelength|Ranges #22 = 596.78571700000043-605.68393200000048
Information|Image|Channel|DetectionWavelength|Ranges #23 = 605.68393200000048-614.58214700000042
Information|Image|Channel|DetectionWavelength|Ranges #24 = 614.58214700000042-623.48036200000047
Information|Image|Channel|DetectionWavelength|Ranges #25 = 623.48036200000047-632.37857700000052
Information|Image|Channel|DetectionWavelength|Ranges #26 = 632.37857700000052-641.27679200000057
Information|Image|Channel|DetectionWavelength|Ranges #27 = 641.27679200000057-650.17500700000051
Information|Image|Channel|DetectionWavelength|Ranges #28 = 650.17500700000051-659.07322200000056
Information|Image|Channel|DetectionWavelength|Ranges #29 = 659.07322200000056-667.97143700000061
Information|Image|Channel|DetectionWavelength|Ranges #30 = 667.97143700000061-676.86965200000054
Information|Image|Channel|DetectionWavelength|Ranges #31 = 676.86965200000054-685.76786700000059
Information|Image|Channel|DetectionWavelength|Ranges #32 = 685.76786700000059-694.66608200000064

*/