//====================================================
macro "Assign Colors to Zeiss Z series [F4]" {
  requires("1.47n");
run("Select None");
//run("Stack to Hyperstack...", "order=xyczt(default) channels=3 slices=1 frames=1 display=Composite");
  Stack.setChannel(1);
  run("Blue");
resetMinAndMax();
  Stack.setChannel(2);
  run("Green");
resetMinAndMax();
  Stack.setChannel(4);
  run("Red");
resetMinAndMax();
  Stack.setDisplayMode("composite");
  Stack.setActiveChannels("1101");
}

//==================================================
macro "Assign Colors to Zeiss Z series and Max Project" {
  requires("1.47n");
  Stack.setChannel(1);
  run("Green");
  Stack.setChannel(2);
  run("Blue");
  Stack.setChannel(4);
  run("Red");
  Stack.setDisplayMode("composite");
  Stack.setActiveChannels("1101");
  run("Median...", "radius=0.5");
  run("Median...", "radius=0.5");
  run("RGB Color", "slices");
  s = nSlices();
  run("Z Project...", "start=1 stop="+s+" projection=[Max Intensity]");
}












//===================================================
macro "Split Channels" {
  requires("1.47n");
  run("Select None");
  run("Split Channels");
  //close();
  //close();
  //setSlice(round(nSlices()/2));
}




//========================================================
//  This macro thresholds the nuclei so that nuclei voxels are 255 and background 0.
//
macro "Prep Nuclei for Measurement"  {
  requires("1.47n");
  run("Select None");
  title = getTitle();
  title = substring(title, 3);
  whereWeAreNow = getSliceNumber();
  s = nSlices();
  run("Duplicate...", "title=[" + title + "] duplicate range=1-"+s+"");
  setSlice(whereWeAreNow);
  run("Median...", "radius=6 stack");
  setAutoThreshold("Default dark");
  setOption("BlackBackground", true);
  run("Convert to Mask", "method=Default background=Dark black");
  convertMaskTo32bits();
  setMinAndMax(0, 1);
  run("Z Project...", "start=1 stop="+s+" projection=[Max Intensity]");
  setMinAndMax(0, 1);
  roiManager("reset");
  // each nucleus marked
  // box around each
  // count the white voxels of each and mult by dx dy dz     run("Histogram", "stack");
}


//=====================================================================
macro "Convert Mask to 0 and 1" { convertMaskTo32bits(); }

function convertMaskTo32bits() {
  requires("1.47n");
  run("Select None");
  run("32-bit");
  run("Divide...", "value=255.000 stack");
  setMinAndMax(0, 1);
  run("Save");
}   // convertMaskTo32bits() 

//=====================================================================
/=========================================================
//  This macro measures the INTENSITIES and VOLUMES of nuclei that are enclosed in ROIs
//  listed in the ROI Manager.
//  If running on a MASK, ignore the intensities.
//
macro "Measure Intensities of Volumes"{
   requires("1.47n");
   getVoxelSize(X, Y, Z, unit);
   print(getTitle + "_nucleus# \t  pixels \t  cubic"+unit + " \t  intensitySum  \t Mean" );
   for (i=0;  i<roiManager("count");  i++){
      roiManager("select", i);
      volumeSum = 0;
      intensitySum = 0;
      for (s=1; s<=nSlices; s++) {
        setSlice(s);
        getHistogram(values, counts, 65536, 0, 65535);
        for (k=1; k<=65535; k++) {
          volumeSum = volumeSum + counts[k];
          intensitySum = intensitySum + (k * counts[k]);
        } //k
      } // for s
      //print(getTitle+"_nucleus_#"+i+" \t "+volumeSum+" \t pixels \t "+volumeSum*X*Y*Z+" \t cubic"+unit + " \t"+ intensitySum + "\t "+ round(intensitySum/volumeSum) );
      print(""+i+" \t "+volumeSum+" \t  "+volumeSum*X*Y*Z+" \t  "+ intensitySum + "\t "+ round(intensitySum/volumeSum) );
    }  // for  i
} // measure

//================================================================================================
//  This macro requires as input a multichannel Z stack.  Typically this will come from a confocal.
//  How to use this:
//  * Have traced cells in the ROI Manager.
//  * Adjust each channel of the multichannel Z stack the way you want it to look.
//  * Run this macro.
//  * Then run the Image > Stacks > Make Montage command
macro "Make vertical & horizontal reslices HYPERSTACK VERSION" {
  requires("1.47i");
  boxWidth = 4;  // how many pixels wide the reslice is; user may change this
  run("Colors...", "foreground=white background=black selection=yellow");
  title = getTitle();
  original = getImageID();
  getVoxelSize(XYscale, XYscale, Zscale, unit);
  //Stack.setDisplayMode("composite");
  if (!(isOpen("ROI Manager"))) exit("Must have ROI Manager open and populated.");
  roiManager("Remove Slice Info");
  run("Set Measurements...", "  centroid bounding redirect=None decimal=3");
  for (i=0;  i<roiManager("count");  i++){
    selectImage(original);
    roiManager("select", i);
    run("Measure");
    xc = getResult("X", nResults-1) / XYscale;
    yc = getResult("Y", nResults-1) / XYscale;
    bx = getResult("BX", nResults-1) / XYscale;
    by = getResult("BY", nResults-1) / XYscale;
    bw = getResult("Width", nResults-1) / XYscale;
    bh = getResult("Height", nResults-1) / XYscale;
    // slice from top
    makeRectangle(bx, yc-(boxWidth/2), bw, boxWidth);
    run("Reslice [/]...", "output="+XYscale+" start=Top");
    temp = getImageID();
    run("Z Project...", "start=1 stop=999 projection=[Max Intensity]");
    temp2 = getImageID();  
    run("RGB Color", "slices");
    selectImage(temp);  close(); 
    selectImage(temp2);  close(); 
    // slice from left
    selectImage(original);
    makeRectangle(xc-(boxWidth/2), by, boxWidth, bh);
    run("Reslice [/]...", "output="+XYscale+" start=Left");
    temp = getImageID();
    run("Z Project...", "start=1 stop=999 projection=[Max Intensity]");
    temp2 = getImageID();  
    run("RGB Color", "slices");
    selectImage(temp);  close(); 
    selectImage(temp2);  close(); 
  }  // for  i   
  run("Images to Stack", "method=[Copy (center)] name=Stack title=MAX use");
  run("Flip Vertically", "stack");
  rename(title + " resliced");
}  // end Make vertical & horizontal reslices

//================================================================================================
//  This macro requires as input a multichannel Z stack.  Typically this will come from a confocal.
//  How to use this:
//  * Have traced cells in the ROI Manager.
//  * Adjust each channel of the multichannel Z stack the way you want it to look.
//  * Run this macro.
//  * Then run the Image > Stacks > Make Montage command
macro "Make vertical & horizontal reslices NOT HYPERSTACK" {
  requires("1.47n");
  boxWidth = 4;  // how many pixels wide the reslice is; user may change this
  run("Colors...", "foreground=white background=black selection=yellow");
  title = getTitle();
  original = getImageID();
  getVoxelSize(XYscale, XYscale, Zscale, unit);
  //Stack.setDisplayMode("composite");
  if (!(isOpen("ROI Manager"))) exit("Must have ROI Manager open and populated.");
  roiManager("Remove Slice Info");
  run("Set Measurements...", "  centroid bounding redirect=None decimal=3");
  for (i=0;  i<roiManager("count");  i++){
    selectImage(original);
    roiManager("select", i);
    run("Measure");
    xc = getResult("X", nResults-1) / XYscale;
    yc = getResult("Y", nResults-1) / XYscale;
    bx = getResult("BX", nResults-1) / XYscale;
    by = getResult("BY", nResults-1) / XYscale;
    bw = getResult("Width", nResults-1) / XYscale;
    bh = getResult("Height", nResults-1) / XYscale;
    // slice from top
    makeRectangle(bx, yc-(boxWidth/2), bw, boxWidth);
    run("Reslice [/]...", "output="+XYscale+" start=Top");
    temp = getImageID();
    run("Z Project...", "start=1 stop=999 projection=[Max Intensity]");
    //temp2 = getImageID();  
    //run("RGB Color", "slices");
    selectImage(temp);  close(); 
    //selectImage(temp2);  close(); 
    // slice from left
    selectImage(original);
    makeRectangle(xc-(boxWidth/2), by, boxWidth, bh);
    run("Reslice [/]...", "output="+XYscale+" start=Left");
    temp = getImageID();
    run("Z Project...", "start=1 stop=999 projection=[Max Intensity]");
    //temp2 = getImageID();  
    //run("RGB Color", "slices");
    selectImage(temp);  close(); 
    //selectImage(temp2);  close(); 
  }  // for  i   
  run("Images to Stack", "method=[Copy (center)] name=Stack title=MAX use");
  run("Flip Vertically", "stack");
  rename(title + " resliced");
}  // end Make vertical & horizontal reslices


//===============================================

macro "Make box at cursor location [q]"{
  width = 175;
  getCursorLoc(x, y, fubar, dummy);
  makeRectangle(x-(width/2), y-(width/2), width, width);
}