// Jan Wisniewski, Experimental Immunology Branch, NCI/NIH, Bethesda MD
// This Macro automatically recognizes Z-stacks and and applies MaxIP tiff
// converts 3 channel ZEN or ND2 images
// saves 16-bit tiff, RGB and composite versions into separate folders

// Note: Please enable File/Import/Bio-Formats(Windowless)

//create custom table
title1 = "Processing Summary"; 
title2 = "["+title1+"]"; 
f=title2; 
run("New... ", "name="+title2+" type=Table"); 
print(f,"\\Headings:Image\tZ_Number\tMaxInt_Projection?\tTarget/Label\tDisplay_Color\tOriginal_Width_(um)\tOriginal_Height(um)\tCropping_Factor\tContrast_Method\tLower_Limit\tUpper_Limit"); 

//  specify folders
Dialog.create("Output and Input Folders");
Dialog.addCheckbox("Save Original Images as 16-bit Tiff", true);
items1 = newArray("Yes", "No");
Dialog.addRadioButtonGroup("Are Those Images Multichannel?", items1, 1, 2, "Yes");
items2 = newArray("Yes", "No");
Dialog.addRadioButtonGroup("If YES, Would You Like to Save Individual Channels Separately?", items2, 1, 2, "No");
items3 = newArray("Yes", "No");
Dialog.addRadioButtonGroup("If Z-stacks, Would You Like to Save Them as AVI as well?", items3, 1, 2, "No");
Dialog.setLocation(1300,800);
Dialog.show(); 
tif16=Dialog.getCheckbox();
multi=Dialog.getRadioButton();
selct=Dialog.getRadioButton();
avi=Dialog.getRadioButton();
	if(selct=="Yes") {splt=1; }
	else {splt=0; }
		if(avi=="Yes") {mov=1;
						ext=".avi";}
		else {mov=0; }
	if(tif16==1) {output2=getDirectory("Choose a Destination for 16-bit Tifs"); }
	if(splt==1)  {output4=getDirectory("_Choose a Destination for Split 16-bit Channels"); }
	if(mov==1) {outputavi=getDirectory("_Choose_a Destination for AVI Files"); }

if(multi=="No") {output1=getDirectory("Choose_a Destination for 8-bit Tifs");	}
output3=getDirectory("Choose__a Destination for Montage");
input=getDirectory("Select a Source Directory");
NAMES=getFileList(input);

setTool("rectangle");
run("Set Measurements...", "modal min bounding display redirect=None decimal=2");

//define functions
function channel_set() {run("Enhance Contrast", "saturated=0.10");
//	Dialog.create("Title");
	Dialog.addString("Enter Dye and/or Target ID", " ");
	items = newArray("B&W", "Blue", "Cyan", "Green", "Yellow", "Red", "Magenta");
	Dialog.addRadioButtonGroup("Display This Channel as:", items, 1, 7, "B&W");
	Dialog.addCheckbox("Exclude This Channel From Color Composite (It will be Shown Separately)", false);
	Dialog.addCheckbox("Highlight Cell Details (if Tramsmitted Light Image)", false);
	Dialog.addCheckbox("Use Only Selected Planes instead of MaxIP of Whole Z-Stack", false);
	Dialog.setLocation(1300,800);
	Dialog.show(); }
function mansc() {run("Brightness/Contrast...");
	waitForUser("Adjust Brightness/Contrast Using B&C Tool Before Proceeding !");
	Dialog.create("Manual B&C Limits");
	Dialog.addNumber("Enter Low Limit:", 0);
	Dialog.addString("Enter High Limit:", "4095");
	Dialog.setLocation(1300,800);
	Dialog.show(); }
function crop_sz() {if(channels>1) {run("Brightness/Contrast...");
	waitForUser("Select Relevant Channel and Autoscale Brightness and Contrast Before Proceeding !"); }
	if(channels==1) {
		}
	Dialog.create("Crop_Size");
	Dialog.addString("Enter Fraction of the Image  (Use 1 for Full Size)", " ");
	Dialog.setLocation(1300,800);
	Dialog.show(); }
function crop_it() {run("Select All");
	run("Scale... ", "x=cr_sz y=cr_sz centered");
	waitForUser("Move Rectangle over the Area of Interest Before Proceeding - Do Not Change Aspect Ratio!");
	run("Crop");
	run("Select None");
	print("Cropped image:   ", cr_sz, "x", cr_sz); }
function autosc() {run("Enhance Contrast", "saturated=0.10");
	run("Gamma...", "value=0.99");
	run("Measure"); }
function autodic() {run("Bandpass Filter...", "filter_large=10 filter_small=3 suppress=None tolerance=5");
	run("Enhance Contrast", "saturated=0.35");
	run("Gamma...", "value=0.99");
	run("Measure"); }
function flatstack() {rename("z");
	run("Z Project...", "projection=[Max Intensity]");
	close("z"); }
function stackDefine() {run("Brightness/Contrast...");
	waitForUser("Inspect Stack to Decide Which Slices to Use");
	Dialog.create("Select Slices");
	Dialog.addNumber("Starting Plane:", 0);
	Dialog.addNumber("How Many Planes to Use Altogether?", 1);
	items2=newArray("All Channels", "This Channel Only");
	Dialog.addRadioButtonGroup("Use Those Planes for:", items2, 1, 2, "This Channel Only");
	Dialog.setLocation(1300,800);
	Dialog.show();	}
function stackSelect() {rename("t");
	run("Slice Keeper", "first=strt last=rend increment=1");
	rename("q");
	close("t"); }
	
//open sample image
showMessage("Open Sample Image to Test Brightness/Contrast");
open();
rename("y");
getDimensions(width, height, channels, slices, frames);
chns=channels;
print("CH:", chns, "   ", "Z:", slices);

// set channels

if(chns==1) {if(slices>1) {run("Brightness/Contrast...");
	waitForUser("Move to the Central/Best Z-slice and adjust B&C");	}
run("Enhance Contrast", "saturated=0.10"); 
Dialog.create("Channel_1");
	channel_set();
	C1=Dialog.getString();
	CX1=Dialog.getRadioButton();
		if(CX1=="B&W") {CC1="Grays"; }
		else {CC1=CX1; }
	CE1=Dialog.getCheckbox();
		CT1=Dialog.getCheckbox();
			CTC1=Dialog.getCheckbox();
	print("Channel_1:   ", C1, "   Displayed_as:   ", CC1, "   Exclude?", CE1, "   Trans?", CT1, "   Center Z?", CTC1); 
run(CC1);
brcon=getBoolean("Is Automatic Brightness/Contrast OK?", "Yes", "Try Manual");
		if(brcon==1) {
		}
		else {mansc();
		valmin=Dialog.getNumber();
		valmax=Dialog.getString();
		function sca() {setMinAndMax(valmin, valmax);
		print("Manual Scaling Range:  ", valmin, "  to  ", valmax); }
		}
close("y"); }

if(chns>1) {if(slices>1) {run("Brightness/Contrast...");
	waitForUser("Move to the Central/Best Z-slice and adjust B&C");
	run("Split Channels"); }
	else {run("Split Channels");	}	
		
selectWindow("C1-y");
run("Enhance Contrast", "saturated=0.10"); 
Dialog.create("Channel_1");
	channel_set();
	C1=Dialog.getString();
	CX1=Dialog.getRadioButton();
		if(CX1=="B&W") {CC1="Grays"; }
		else {CC1=CX1; }
	CE1=Dialog.getCheckbox();
		CT1=Dialog.getCheckbox();
			CTC1=Dialog.getCheckbox();
	print("Channel_1:   ", C1, "   Displayed_as:   ", CC1, "   Exclude?", CE1, "   Trans?", CT1, "   Center Z?", CTC1); 
run(CC1);
brcon1=getBoolean("Is Automatic Brightness/Contrast OK?", "Yes", "Try Manual");
	if(brcon1==1) {
	}
	else {mansc();
		valmin1=Dialog.getNumber();
		valmax1=Dialog.getString();	
	function sca1() {setMinAndMax(valmin1, valmax1);
	print("Channel_1 Manual Range:  ", valmin1, "  to  ", valmax1); }
	}
close ("C1-y");

selectWindow("C2-y");
run("Enhance Contrast", "saturated=0.10"); 
Dialog.create("Channel_2");
	channel_set();
	C2=Dialog.getString();
	CX2=Dialog.getRadioButton();
		if(CX2=="B&W") {CC2="Grays"; }
		else {CC2=CX2; }
	CE2=Dialog.getCheckbox();
		CT2=Dialog.getCheckbox();
			CTC2=Dialog.getCheckbox();
	print("Channel_2:   ", C2, "   Displayed_as:   ", CC2, "   Exclude?", CE2, "   Trans?", CT2, "   Center Z?", CTC2);
run(CC2);
brcon2=getBoolean("Is Automatic Brightness/Contrast OK?", "Yes", "Try Manual");
if(brcon2==1) {
	}
else {mansc();
		valmin2=Dialog.getNumber();
		valmax2=Dialog.getString();
	function sca2() {setMinAndMax(valmin2, valmax2);
	print("Channel_2 Manual Range:  ", valmin2, "  to  ", valmax2); }
	}
close ("C2-y"); }

if(chns>2) {selectWindow("C3-y");
run("Enhance Contrast", "saturated=0.10"); 
Dialog.create("Channel 3");
	channel_set();
	C3=Dialog.getString();
	CX3=Dialog.getRadioButton();
		if(CX3=="B&W") {CC3="Grays"; }
		else {CC3=CX3; }
	CE3=Dialog.getCheckbox();
		CT3=Dialog.getCheckbox();
			CTC3=Dialog.getCheckbox();
	print("Channel_3:   ", C3, "   Displayed_as:   ", CC3, "   Exclude?", CE3, "   Trans?", CT3, "   Center Z?", CTC3); 
run(CC3);
brcon3=getBoolean("Is Automatic Brightness/Contrast OK?", "Yes", "Try Manual");
	if(brcon3==1) {
	}
	else {mansc();
		valmin3=Dialog.getNumber();
		valmax3=Dialog.getString();
	function sca3() {setMinAndMax(valmin3, valmax3);
	print("Channel_3 Manual Range:  ", valmin3, "  to  ", valmax3); }
	}
close ("C3-y"); }

if(chns>3) {selectWindow("C4-y");
run("Enhance Contrast", "saturated=0.10"); 
Dialog.create("Channel_4");
	channel_set();
	C4=Dialog.getString();
	CX4=Dialog.getRadioButton();
		if(CX4=="B&W") {CC4="Grays"; }
		else {CC4=CX4; }
	CE4=Dialog.getCheckbox();
		CT4=Dialog.getCheckbox();
			CTC4=Dialog.getCheckbox();
	print("Channel_4:   ", C4, "   Displayed_as:   ", CC4, "   Exclude?", CE4, "   Trans?", CT4, "   Center Z?", CTC4); 
run(CC4);
brcon4=getBoolean("Is Automatic Brightness/Contrast OK?", "Yes", "Try Manual");
	if(brcon4==1) {
	}
	else {mansc();
		valmin4=Dialog.getNumber();
		valmax4=Dialog.getString();
	function sca4() {setMinAndMax(valmin4, valmax4);
	print("Channel_4 Manual Range:  ", valmin4, "  to  ", valmax4); }
	}
close ("C4-y"); }

if(chns>4) {selectWindow("C5-y");
run("Enhance Contrast", "saturated=0.10"); 
Dialog.create("Channel_5");
	channel_set();
	C5=Dialog.getString();
	CX5=Dialog.getRadioButton();
		if(CX5=="B&W") {CC5="Grays"; }
		else {CC5=CX5; }
	CE5=Dialog.getCheckbox();
		CT5=Dialog.getCheckbox();
			CTC5=Dialog.getCheckbox();
	print("Channel_5:   ", C5, "   Displayed_as:   ", CC5, "   Exclude?", CE5, "   Trans?", CT5, "   Center Z?", CTC5);
run(CC5);
brcon5=getBoolean("Is Automatic Brightness/Contrast OK?", "Yes", "Try Manual");
	if(brcon5==1) {
	}
	else {mansc();
		valmin5=Dialog.getNumber();
		valmax5=Dialog.getString();
	function sca5() {setMinAndMax(valmin5, valmax5);
	print("Channel_5 Manual Range:  ", valmin5, "  to  ", valmax5); }
	}
close ("C5-y"); }

if(chns>5) {selectWindow("C6-y");
run("Enhance Contrast", "saturated=0.10"); 
Dialog.create("Channel_6");
	channel_set();
	C6=Dialog.getString();
	CX6=Dialog.getRadioButton();
		if(CX6=="B&W") {CC6="Grays"; }
		else {CC6=CX6; }
	CE6=Dialog.getCheckbox();
		CT6=Dialog.getCheckbox();
			CTC6=Dialog.getCheckbox();
	print("Channel_6:   ", C6, "   Displayed_as:   ", CC6, "   Exclude?", CE6, "   Trans?", CT6, "   Center Z?", CTC6); 
run(CC6);
brcon6=getBoolean("Is Automatic Brightness/Contrast OK?", "Yes", "Try Manual");
	if(brcon6==1) {
		}
	else {mansc();
		valmin6=Dialog.getNumber();
		valmax6=Dialog.getString();
	function sca6() {setMinAndMax(valmin6, valmax6);
	print("Channel_6 Manual Range:  ", valmin6, "  to  ", valmax6); }
	}
close ("C6-y"); }

if(chns>6) {selectWindow("C7-y");
run("Enhance Contrast", "saturated=0.10"); 
Dialog.create("Channel_7");
	channel_set();
	C7=Dialog.getString();
	CX7=Dialog.getRadioButton();
		if(CX7=="B&W") {CC7="Grays"; }
		else {CC7=CX7; }
	CE7=Dialog.getCheckbox();
		CT7=Dialog.getCheckbox();
			CTC7=Dialog.getCheckbox();
	print("Channel_7:   ", C7, "   Displayed_as:   ", CC7, "   Exclude?", CE7, "   Trans?", CT7, "   Center Z?", CTC7); 
run(CC7);
brcon7=getBoolean("Is Automatic Brightness/Contrast OK?", "Yes", "Try Manual");
if(brcon7==1) {
	}
else {mansc();
		valmin7=Dialog.getNumber();
		valmax7=Dialog.getString();
	function sca7() {setMinAndMax(valmin7, valmax7);
	print("Channel_7 Manual Range:  ", valmin7, "  to  ", valmax7); }
	}
close ("C7-y"); }

//extra info
Dialog.create("Additional Settings");
items = newArray("Yes", "No");
Dialog.addRadioButtonGroup("Would You Like to Crop Individual Images?", items, 1, 2, "No");
Dialog.addChoice("Montage Size reduction", newArray("Full Size", "0.5", "0.33", "0.25"), "0.5");
Dialog.addNumber("Font Size", 25);
Dialog.addString("Scale Bar (microns)", "10");
//Dialog.addCheckbox("Exclude DIC/BF Channel from Color-Composite Panel", false);
Dialog.setLocation(1300,800);
Dialog.show(); 
imcrp=Dialog.getRadioButton;
	if(imcrp=="Yes") {crp=0; }
	else{crp=1; }
mosrdx=Dialog.getChoice();
	if(mosrdx=="Full size") {rdx=1; }
	else{rdx=mosrdx; }
fnt=Dialog.getNumber();
fntbar=2*fnt/3;
lngt=Dialog.getString;
//transm=Dialog.getCheckbox();
print("Image Cropping:   ", imcrp);
print("Montage Size Reduction:   ", mosrdx);
print("Font_Size:  ", fnt, "   Scale_Bar:  ", lngt, "microns   ");
//if(transm==1) {if(channels>1) {print("Transmitted Light Image Excluded from Color-Composite"); }
//			else {
//			}
// }

if(chns>1) {if(CE1==1) {print(C1, " Excluded from Color-Composite"); }
				if(CE2==1) {print(C2, " Excluded from Color-Composite"); }	}
if(chns>2) {if(CE3==1) {print(C3, " Excluded from Color-Composite"); }	}		
if(chns>3) {if(CE4==1) {print(C4, " Excluded from Color-Composite"); }	}	
if(chns>4) {if(CE5==1) {print(C5, " Excluded from Color-Composite"); }	}	
if(chns>5) {if(CE6==1) {print(C6, " Excluded from Color-Composite"); }	}	
if(chns>6) {if(CE7==1) {print(C7, " Excluded from Color-Composite"); }	}	
 
print("   ");
print("Images:");
print("   ");

//process images
for (i=0; i<NAMES.length; i++) {
	open(input+NAMES[i]);
ttl=File.nameWithoutExtension;
	print(ttl);
getDimensions(width, height, channels, slices, frames);
//w=width;
//h=height;
print("Original_Image_Size:   ", width, " x ", height, "   pixels");
run("Measure");
wdt=Table.getString("Width");
hgt=Table.getString("Height");
print("Original_Image_Size:   ", wdt, " x ", hgt, "   microns");
if(tif16==1) {saveAs("Tiff", output2+ttl); }
if(chns==1) {if(slices>1) {if(mov==1) {run("AVI... ", "compression=None frame=10 save=["+outputavi+ttl+ext+"]"); }	}	}
rename("x");
if(chns>1) {if(splt==1) {run("Duplicate...", "duplicate");
			rename("u");
			run("Split Channels");
			selectWindow("C1-u");
			run(CC1);
			saveAs("Tiff", output4+ttl+"-"+CC1);
			if(mov==1) {if(slices>1) {run("AVI... ", "compression=None frame=5 save=["+outputavi+ttl+CC1+ext+"]");}		}
			close();
			selectWindow("C2-u");
			run(CC2);
			saveAs("Tiff", output4+ttl+"-"+CC2);
			if(mov==1) {if(slices>1) {run("AVI... ", "compression=None frame=10 save=["+outputavi+ttl+CC2+ext+"]");}	}

			close();
		if(chns>2) { selectWindow("C3-u");
			run(CC3);
			saveAs("Tiff", output4+ttl+"-"+CC3);
			if(mov==1) {if(slices>1) {run("AVI... ", "compression=None frame=10 save=["+outputavi+ttl+CC3+ext+"]");}	}
			close(); }
		if(chns>3) { selectWindow("C4-u");
			run(CC4);
			saveAs("Tiff", output4+ttl+"-"+CC4);
			if(mov==1) {if(slices>1) {run("AVI... ", "compression=None frame=10 save=["+outputavi+ttl+CC4+ext+"]");}	}
			close(); }
		if(chns>4) { selectWindow("C5-u");
			run(CC5);
			saveAs("Tiff", output4+ttl+"-"+CC5);
			if(mov==1) {if(slices>1) {run("AVI... ", "compression=None frame=10 save=["+outputavi+ttl+CC5+ext+"]");}	}
			close(); }
		if(chns>5) { selectWindow("C6-u");
			run(CC6);
			saveAs("Tiff", output4+ttl+"-"+CC6);
			if(mov==1) {if(slices>1) {run("AVI... ", "compression=None frame=10 save=["+outputavi+ttl+CC6+ext+"]");}	}
			close(); }
		if(chns>6) { selectWindow("C7-u");
			run(CC7);
			saveAs("Tiff", output4+ttl+"-"+CC7);
			if(mov==1) {if(slices>1) {run("AVI... ", "compression=None frame=10 save=["+outputavi+ttl+CC7+ext+"]");}	}
			close(); }			
				}
			}

//process channel 1
run("Enhance Contrast", "saturated=0.10");
if(crp==1) {print("Full image");
			cr_sz="Full"; }
else {
crop_sz();
	cr_sz=Dialog.getString();
	if(cr_sz==1) {print("Full image");
				cr_sz="Full"; }
	else {crop_it(); }
	}
if(chns==1) { labl=C1;
			colr=CC1;

			
	if(slices>1) {print("# of Z-slices:  ", slices);
		if(CTC1==1) {stackDefine();
					strt=Dialog.getNumber();
					rnge=Dialog.getNumber();
					rend=strt+rnge-1;
					some=Dialog.getRadioButton();
					if(some=="All Channels") {chce=1; }
					else {chce=0; }
					print(strt, rnge, rend, chce);
				stackSelect();
				maxip="selected"; }
		else {flatstack();
				rename("x"); 
				maxip="all";}	}
	else { maxip="n/a"; }
if(CT1=="Yes") {autodic();
		minval=Table.getString("Min");
		maxval=Table.getString("Max");
	print("Auto-scaled:   ", minval, "   ", maxval, "   FFT   ");
		meth="Auto";
		l_lim=minval;
		u_lim=maxval; }
else {if (brcon==1) {autosc();
minval=Table.getString("Min");
maxval=Table.getString("Max");
	print("Auto-scaled:   ", minval, "   ", maxval);
	meth="Auto";
	l_lim=minval;
	u_lim=maxval; }
else {sca();
	meth="Manual";
	l_lim=valmin;
	u_lim=valmax;
 		}
	}
if(crp==0) {
			if(cr_sz==1) {
			}
			else {rename("v");
			enl=1/cr_sz;
			run("Scale...", "x=enl y=enl width=w height=h interpolation=Bilinear create");
			print("Resampled to Original Display Size");
			close("v");
			rename("x"); }
				}
else {
	}
run(CC1);
run("Apply LUT");
run("8-bit");
run("Scale Bar...", "width=lngt height=4 font=fntbar color=White background=None location=[Upper Right] bold overlay");
run("Flatten");
saveAs("Tiff", output1+NAMES[i]);
close();
selectWindow("Processing Summary");
print(f,ttl+"\t"+slices+"\t"+maxip+"\t"+labl+"\t"+colr+"\t"+wdt+"\t"+hgt+"\t"+cr_sz+"\t"+meth+"\t"+l_lim+"\t"+u_lim);
close("x"); }	

if(chns>1) {run("Split Channels");
selectWindow("C1-x");
labl=C1;
colr=CC1;
	if(slices>1) {print("# of Z-slices:  ", slices);
		if(CTC1==1) {stackDefine();
					strt=Dialog.getNumber();
					rnge=Dialog.getNumber();
					rend=strt+rnge-1;
					print(strt, rnge, rend);
				stackSelect();
				maxip="selected"; }
		else {flatstack();
				rename("C1-x"); 
				maxip="all";}	}
	else { maxip="n/a"; }
if(CT1==1) {autodic();
		minval1=Table.getString("Min");
		maxval1=Table.getString("Max");
	print("Channel_1 Auto-scaled:   ", minval1, "   ", maxval1, "   FFT   ");
		meth="Auto";
		l_lim=minval1;
		u_lim=maxval1; }
else {if (brcon1==1) {autosc();
minval1=Table.getString("Min");
maxval1=Table.getString("Max");
	print("Channel_1 Auto-scaled:   ", minval1, "   ", maxval1);
	meth="Auto";
	l_lim=minval1;
	u_lim=maxval1; }
else {sca1();
	meth="Manual";
	l_lim=valmin1;
	u_lim=valmax1; }
	 }
run(CC1);
run("Apply LUT");
run("RGB Color");
rename(C1);
selectWindow("Processing Summary");
print(f,ttl+"\t"+slices+"\t"+maxip+"\t"+labl+"\t"+colr+"\t"+wdt+"\t"+hgt+"\t"+cr_sz+"\t"+meth+"\t"+l_lim+"\t"+u_lim);

selectWindow("C2-x");
	labl=C2;
	colr=CC2;
	if(slices>1) {print("# of Z-slices:  ", slices);
		if(CTC2==1) {stackDefine();
					strt=Dialog.getNumber();
					rnge=Dialog.getNumber();
					rend=strt+rnge-1;
					print(strt, rnge, rend);		
				stackSelect();
				maxip="selected"; }
		else {flatstack();
				rename("C2-x"); 
				maxip="all";}	}
	else { maxip="n/a"; }
if(CT2==1) {autodic();
		minval2=Table.getString("Min");
		maxval2=Table.getString("Max");
	print("Channel_2 Auto-scaled:   ", minval2, "   ", maxval2, "   FFT   ");
		meth="Auto";
		l_lim=minval2;
		u_lim=maxval2; }
else {if (brcon2==1) {autosc();
minval2=Table.getString("Min");
maxval2=Table.getString("Max");
	print("Channel_2 Auto-scaled:   ", minval2, "   ", maxval2);
	meth="Auto";
	l_lim=minval2;
	u_lim=maxval2; }
else {sca2();
	meth="Manual";
	l_lim=valmin2;
	u_lim=valmax2; }
	 }
run(CC2);
run("Apply LUT");
run("RGB Color");
rename(C2);
selectWindow("Processing Summary");
print(f," "+"\t"+" "+"\t"+maxip+"\t"+labl+"\t"+colr+"\t"+" "+"\t"+" "+"\t"+" "+"\t"+meth+"\t"+l_lim+"\t"+u_lim); }
 
if(chns>2) {selectWindow("C3-x");
	labl=C3;
	colr=CC3;
	if(slices>1) {print("# of Z-slices:  ", slices);
		if(CTC3==1) {stackDefine();
				stackSelect();
				maxip="selected"; }
		else {flatstack();
				rename("C3-x"); 
				maxip="all";}	}
	else { maxip="n/a"; }
if(CT3==1) {autodic();
		minval3=Table.getString("Min");
		maxval3=Table.getString("Max");
	print("Channel_3 Auto-scaled:   ", minval3, "   ", maxval3, "   FFT   ");
		meth="Auto";
		l_lim=minval3;
		u_lim=maxval3; }
else {if (brcon3==1) {autosc();
minval3=Table.getString("Min");
maxval3=Table.getString("Max");
	print("Channel_3 Auto-scaled:   ", minval3, "   ", maxval3);
	meth="Auto";
	l_lim=minval3;
	u_lim=maxval3; }
else {sca3();
	meth="Manual";
	l_lim=valmin3;
	u_lim=valmax3; }
	 }
run(CC3);
run("Apply LUT");
run("RGB Color");
rename(C3);
selectWindow("Processing Summary");
print(f," "+"\t"+" "+"\t"+maxip+"\t"+labl+"\t"+colr+"\t"+" "+"\t"+" "+"\t"+" "+"\t"+meth+"\t"+l_lim+"\t"+u_lim); }

if(chns>3) {selectWindow("C4-x");
	labl=C4;
	colr=CC4;
	if(slices>1) {print("# of Z-slices:  ", slices);
		if(CTC4==1) {stackDefine();
				stackSelect();
				maxip="selected"; }
		else {flatstack();
				rename("C4-x"); 
				maxip="all";}	}
	else { maxip="n/a"; }
if(CT4==1) {autodic();
		minval4=Table.getString("Min");
		maxval4=Table.getString("Max");
	print("Channel_4 Auto-scaled:   ", minval4, "   ", maxval4, "   FFT   ");
		meth="Auto";
		l_lim=minval4;
		u_lim=maxval4; }
else {
if (brcon4==1) {autosc();
minval4=Table.getString("Min");
maxval4=Table.getString("Max");
	print("Channel_4 Auto-scaled:   ", minval4, "   ", maxval4);
	meth="Auto";
	l_lim=minval4;
	u_lim=maxval4; }
else {sca4();
	meth="Manual";
	l_lim=valmin4;
	u_lim=valmax4; }
	}
run(CC4);
run("Apply LUT");
run("RGB Color");
rename(C4);
selectWindow("Processing Summary");
print(f," "+"\t"+" "+"\t"+maxip+"\t"+labl+"\t"+colr+"\t"+" "+"\t"+" "+"\t"+" "+"\t"+meth+"\t"+l_lim+"\t"+u_lim); }

if(chns>4) {selectWindow("C5-x");
	labl=C5;
	colr=CC5;
	if(slices>1) {print("# of Z-slices:  ", slices);
		if(CTC5==1) {stackDefine();
				stackSelect();
				maxip="selected"; }
		else {flatstack();
				rename("C5-x"); 
				maxip="all";}	}
	else { maxip="n/a"; }
if(CT5==1) {autodic();
		minval5=Table.getString("Min");
		maxval5=Table.getString("Max");
	print("Channel_5 Auto-scaled:   ", minval5, "   ", maxval5, "   FFT   ");
		meth="Auto";
		l_lim=minval5;
		u_lim=maxval5; }
else {
if (brcon5==1) {autosc();
minval5=Table.getString("Min");
maxval5=Table.getString("Max");
	print("Channel_5 Auto-scaled:   ", minval5, "   ", maxval5);
	meth="Auto";
	l_lim=minval5;
	u_lim=maxval5; }
else {sca5();
	meth="Manual";
	l_lim=valmin5;
	u_lim=valmax5; }
	}
run(CC5);
run("Apply LUT");
run("RGB Color");
rename(C5);
selectWindow("Processing Summary");
print(f," "+"\t"+" "+"\t"+maxip+"\t"+labl+"\t"+colr+"\t"+" "+"\t"+" "+"\t"+" "+"\t"+meth+"\t"+l_lim+"\t"+u_lim); }

if(chns>5) {selectWindow("C6-x");
	labl=C6;
	colr=CC6;
	if(slices>1) {print("# of Z-slices:  ", slices);
		if(CTC6==1) {stackDefine();
				stackSelect();
				maxip="selected"; }
		else {flatstack();
				rename("C6-x"); 
				maxip="all";}	}
	else { maxip="n/a"; }
if(CT6==1) {autodic();
		minval6=Table.getString("Min");
		maxval6=Table.getString("Max");
	print("Channel_6 Auto-scaled:   ", minval6, "   ", maxval6, "   FFT   ");
		meth="Auto";
		l_lim=minval6;
		u_lim=maxval6; }
else {
if (brcon6==1) {autosc();
minval6=Table.getString("Min");
maxval6=Table.getString("Max");
	print("Channel_6 Auto-scaled:   ", minval6, "   ", maxval6);
	meth="Auto";
	l_lim=minval6;
	u_lim=maxval6; }
else {sca6();
	meth="Manual";
	l_lim=valmin6;
	u_lim=valmax6; }
	}
run(CC6);
run("Apply LUT");
run("RGB Color");
rename(C6);
selectWindow("Processing Summary");
print(f," "+"\t"+" "+"\t"+maxip+"\t"+labl+"\t"+colr+"\t"+" "+"\t"+" "+"\t"+" "+"\t"+meth+"\t"+l_lim+"\t"+u_lim); }

if(chns>6) {selectWindow("C7-x");
	labl=C7;
	colr=CC7;
	if(slices>1) {print("# of Z-slices:  ", slices);
		if(CTC7==1) {stackDefine();
				stackSelect();
				maxip="selected"; }
		else {flatstack();
				rename("C7-x"); 
				maxip="YES";}	}
	else { maxip="n/a"; }
if(CT7==1) {autodic();
		minval7=Table.getString("Min");
		maxval7=Table.getString("Max");
	print("Channel_7 Auto-scaled:   ", minval7, "   ", maxval7, "   FFT   ");
		meth="Auto";
		l_lim=minval7;
		u_lim=maxval7; }
else {
if (brcon7==1) {autosc();
minval7=Table.getString("Min");
maxval7=Table.getString("Max");
	print("Channel_7 Auto-scaled:   ", minval7, "   ", maxval7);
	meth="Auto";
	l_lim=minval7;
	u_lim=maxval7; }
else {sca7();
	meth="Manual";
	l_lim=valmin7;
	u_lim=valmax7; }
	}
run(CC7);
run("Apply LUT");
run("RGB Color");
rename(C7);
selectWindow("Processing Summary");
print(f," "+"\t"+" "+"\t"+maxip+"\t"+labl+"\t"+colr+"\t"+" "+"\t"+" "+"\t"+" "+"\t"+meth+"\t"+l_lim+"\t"+u_lim); }
print("   ");

//if(channels>1) {if(transm==1) {run("Images to Stack", "name=All title=[] use keep");
//	selectWindow("DIC/BF");
//	close();
//	run("Images to Stack", "name=Comp title=[] use");
//	run("Z Project...", "projection=[Max Intensity]");
//	rename(NAMES[i]);
//	saveAs("Tiff", output1+NAMES[i]);
//	selectWindow("Comp");
//	close();
//	selectWindow("All");
//	run("Stack to Images");
//	run("Images to Stack", "name=Stack title=[] use");}

if(chns>1) {run("Images to Stack", "name=All title=[] use keep");
	if(CE1==1) {close(C1); }
	if(CE2==1) {close(C2); }
	if(chns>2) {if(CE3==1) {close(C3); }	}
	if(chns>3) {if(CE4==1) {close(C4); }	}
	if(chns>4) {if(CE5==1) {close(C5); }	}
	if(chns>5) {if(CE6==1) {close(C6); }	}
	if(chns>6) {if(CE7==7) {close(C7); }	}
	run("Images to Stack", "name=Comp title=[] use");
	run("Z Project...", "projection=[Max Intensity]");
	rename(NAMES[i]);
//	saveAs("Tiff", output1+NAMES[i]);
//	selectWindow("Comp");
//	close();
	selectWindow("All");
	run("Stack to Images");
	run("Images to Stack", "name=Stack title=[] use");
	getDimensions(width, height, channels, slices, frames);
	if(slices<4) {rws=1;
				clm=slices;	}
	else {rws=0.75+slices/4;
		rows=rws;
		clm=4;	}

//	else {run("Images to Stack", "name=Stack title=[] use");
//	run("Z Project...", "projection=[Max Intensity]");
//	rename(NAMES[i]);
//	saveAs("Tiff", output1+NAMES[i]);
//	selectWindow("Stack");
//	run("Stack to Images");
//	run("Images to Stack", "name=Stack title=[] use"); }
	
//if(channels==2) {run("Make Montage...", "columns=3 rows=1 scale=rdx border=2 font=fnt label"); }
//if(channels==3) {run("Make Montage...", "columns=2 rows=2 scale=rdx border=2 font=fnt label"); }
//if(channels==4) {run("Make Montage...", "columns=3 rows=2 scale=rdx border=2 font=fnt label"); }
//if(channels==5) {run("Make Montage...", "columns=3 rows=1 scale=rdx border=2 font=fnt label"); }
//if(channels==6) {run("Make Montage...", "columns=4 rows=2 scale=rdx border=2 font=fnt label"); }
//if(channels==7) {run("Make Montage...", "columns=4 rows=2 scale=rdx border=2 font=fnt label"); }

run("Make Montage...", "columns=clm rows=rws scale=rdx border=2 font=fnt label");
run("Scale Bar...", "width=lngt height=4 font=fntbar color=White background=None location=[Upper Right] bold overlay");
run("Flatten");
saveAs("Tiff", output3+NAMES[i]); 
close();
close();
close();
close();
}

if(chns==1) {LIST=getFileList(output1);
	for (i=0; i<LIST.length; i++) {
	open(output1+LIST[i]);}
run("Images to Stack", "name=Stack title=[] use");
rws=0.75+nSlices/4;
run("Make Montage...", "columns=4 rows=rws scale=rdx border=2 font=fnt label");
rename("Composite");
saveAs("Tiff", output3+"Composite");
close();
close(); }
}
selectWindow("Processing Summary");
saveAs("Text", output3+"Processing Summary.csv");
close("Processing Summary");
selectWindow("Log");
saveAs("Text", output3+"Log.txt");
close("Log");
close("Results");