//Jan Wisniewski, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA

//This macro requires separated mosaic tiles.
//The mosaic should include some empty area around a tissue section or at least on empty field, so the macro can extract flat field data.
//All tiles are flat-field and color balance corrected prior to row-by-row assembly.
//There is an option to just annotate already assembled mosaics or re-start process from intermediate stages.
//To establish tile offsets, this macro use "Pairwise Stitching" plug-in (Preibisch et al., Bioinformatics(2009) 25(11) 1463-65) present in Fiji installation of ImageJ.
//Mosaics are saved as three-channel 16-bit tif and RGB image

print("Histological image mosaic correction and display\nJan Wisniewski, Experimental Immunology Branch\nNational Cancer Institute, NIH, Bethesda, Maryland");
getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
print("");
print("run: ", month, "/", dayOfMonth, "/", year, "   at ", hour, ":", minute);
print("");

run("Set Measurements...", "area mean min integrated median display scientific redirect=None decimal=0");

prc=getBoolean("Do you want to process a set of already assembled mosaics, stored in a separate folder?");
if(prc==0)	{Dialog.create("Already assembled tiles options");
			Dialog.addMessage("Check all that apply:");
			Dialog.addCheckbox("Check if you already have corrected tiles", false);
			Dialog.addCheckbox("Check if they are sorted into subfolders according to the mosaic row", false);
			Dialog.addCheckbox("Check if rows are padded to equal length", false);
			Dialog.show();
			res=Dialog.getCheckbox();
			srt=Dialog.getCheckbox();
			pdd=Dialog.getCheckbox();	

if(res==0)	{mscs=getBoolean("Do you want to store copies of all mosaic in a single folder?");
	if(mscs==1) {mosaics=getDirectory("Select Folder to store copies of all mosaics");	}

output=getDirectory("Choose_Directory for Results and temporary Directories");
myDir0 = output+"scale applied"+File.separator;
File.makeDirectory(myDir0);
myDir1 = output+"red"+File.separator;
File.makeDirectory(myDir1);
myDir2 = output+"grn"+File.separator;
File.makeDirectory(myDir2);
myDir3 = output+"blu"+File.separator;
File.makeDirectory(myDir3);
myDir4 = output+"tiles"+File.separator;
File.makeDirectory(myDir4);
myDir5 = output+"stripes"+File.separator;
File.makeDirectory(myDir5);
myDir6 = output+"corr-red"+File.separator;
File.makeDirectory(myDir6);
myDir7 = output+"corr-grn"+File.separator;
File.makeDirectory(myDir7);
myDir8 = output+"corr-blu"+File.separator;
File.makeDirectory(myDir8);
input=getDirectory("Select a Source Directory");
NAMES=getFileList(input);

Dialog.create("Image scale");
Dialog.addNumber("Objective magnification:", 10);
items=newArray("AxioCam MRc5", "Orca Flash 4.0", "other");
Dialog.addChoice("Camera used:", items, "AxioCam MRc5");
Dialog.addNumber("If OTHER, type detector's pixel size:", 0);
Dialog.show();
obj=Dialog.getNumber();
cam=Dialog.getChoice();
othp=Dialog.getNumber();
if(cam=="other") {pxl=othp/obj;		}
if(cam=="AxioCam MRc5") {pxl=6.8/obj;	}
if(cam=="Orca Flash 4.0") {pxl=6.5/obj;	}

print("Camera:", cam, " magnification:", obj, "effective pixel size:", pxl);

for (i=0; i<NAMES.length; i++) {j=1101+i;
	open(input+NAMES[i]);
	ttt=File.nameWithoutExtension;
	run("Set Scale...", "distance=1 known=pxl pixel=1 unit=um global");
	saveAs("Tiff", myDir0+ttt);
	close();	}

TNAMES=getFileList(myDir0);
setBatchMode(true);
for (i=0; i<TNAMES.length; i++) {
j=1101+i;
open(myDir0+TNAMES[i]);
ttl=File.nameWithoutExtension;
rename("x");
run("Split Channels");
selectWindow("C1-x");
	saveAs("Tiff", myDir1+j);
	close();
selectWindow("C2-x");
	saveAs("Tiff", myDir2+j);
	close();
selectWindow("C3-x");
	saveAs("Tiff", myDir3+j);
	close();	}

NAMER=getFileList(myDir1);
for (i=0; i<NAMER.length; i++) {
	open(myDir1+NAMER[i]);	}
run("Images to Stack", "name=Stack title=[] use");
run("Z Project...", "projection=[Max Intensity]");
run("Median...", "radius=5");
run("32-bit");
run("Measure");
aver=getResult("Mean");
run("Divide...", "value=aver");
run("Enhance Contrast", "saturated=0.10");
imageCalculator("Divide create stack", "Stack","MAX_Stack");
rename("red");
close("Stack");
close("MAX_Stack");

NAMEG=getFileList(myDir2);
for (i=0; i<NAMEG.length; i++) {
	open(myDir2+NAMEG[i]);	}
run("Images to Stack", "name=Stack title=[] use");
run("Z Project...", "projection=[Max Intensity]");
run("Median...", "radius=5");
run("32-bit");
run("Measure");
aveg=getResult("Mean");
run("Divide...", "value=aver");
run("Enhance Contrast", "saturated=0.10");
imageCalculator("Divide create stack", "Stack","MAX_Stack");
rename("grn");
close("Stack");
close("MAX_Stack");

NAMEB=getFileList(myDir3);
for (i=0; i<NAMEB.length; i++) {
	open(myDir3+NAMEB[i]);	}
run("Images to Stack", "name=Stack title=[] use");
run("Z Project...", "projection=[Max Intensity]");
run("Median...", "radius=5");
run("32-bit");
run("Measure");
aveb=getResult("Mean");
run("Divide...", "value=aver");
run("Enhance Contrast", "saturated=0.10");
imageCalculator("Divide create stack", "Stack","MAX_Stack");
rename("blu");
close("Stack");
close("MAX_Stack");
close("Results");

selectWindow("red");
getDimensions(width, height, channels, slices, frames);
tils=slices;
print(tils);
run("Stack to Images");
for (i=0; i < tils; i++) {j=1100+tils-i;
	saveAs("Tiff", myDir6+j);
	close(); }

selectWindow("grn");
getDimensions(width, height, channels, slices, frames);
tils=slices;
print(tils);
run("Stack to Images");
for (i=0; i < tils; i++) {j=1100+tils-i;
	saveAs("Tiff", myDir7+j);
	close(); }

selectWindow("blu");
getDimensions(width, height, channels, slices, frames);
tils=slices;
print(tils);
run("Stack to Images");
for (i=0; i < tils; i++) {j=1100+tils-i;
	saveAs("Tiff", myDir8+j);
	close(); }

for (g=0; g<TNAMES.length; g++)	
ok = File.delete(myDir0+TNAMES[g]);
ok = File.delete(myDir0);
tlist1=getFileList(myDir1);
for (h=0; h<tlist1.length; h++)	
ok = File.delete(myDir1+tlist1[h]);
ok = File.delete(myDir1);
tlist2=getFileList(myDir2);
for (h=0; h<tlist2.length; h++)	
ok = File.delete(myDir2+tlist2[h]);
ok = File.delete(myDir2);
tlist3=getFileList(myDir3);
for (h=0; h<tlist3.length; h++)	
ok = File.delete(myDir3+tlist3[h]);
ok = File.delete(myDir3);

rlist=getFileList(myDir6);
glist=getFileList(myDir7);
blist=getFileList(myDir8);
for (i = 0; i < rlist.length; i++) {j=1101+i;
open(myDir6+rlist[i]);
run("Red");
rename("C1-x");
open(myDir7+glist[i]);
run("Green");
rename("C2-x");
open(myDir8+blist[i]);
run("Blue");
rename("C3-x");
run("Merge Channels...", "c1=C1-x c2=C2-x c3=C3-x create");
saveAs("Tiff", myDir4+j);
close();			}

for (i=0; i<rlist.length; i++)	
ok = File.delete(myDir6+rlist[i]);
ok = File.delete(myDir6);
for (i=0; i<glist.length; i++)	
ok = File.delete(myDir7+glist[i]);
ok = File.delete(myDir7);
for (i=0; i<blist.length; i++)	
ok = File.delete(myDir8+blist[i]);
ok = File.delete(myDir8);		}

setBatchMode(false);

if(res==1) {mscs=getBoolean("Do you want to store copies of all mosaic in a single folder?";
	if(mscs==1) {mosaics=getDirectory("Select Folder to store copies of all mosaics");	}
	
output=getDirectory("Choose_Directory holding all sufolders with results");
input=getDirectory("Select Directory with original, uncorrected tiles");
NAMES=getFileList(input);
open(input+NAMES[1]);
getDimensions(width, height, channels, slices, frames);
ttl=File.nameWithoutExtension;
close();
myDir5 = output+"stripes"+File.separator;
File.makeDirectory(myDir5);
myDir4=getDirectory("Choose_Directory named TILES");	}

// get offsets
tlist4=getFileList(myDir4);

compl=getBoolean("Do you already know horizontal and vertical offset values?");
if(compl==0) {waitForUser("1) Make Log window larger to see the measurements afterwards\n2) Then identify two tiles adjacent horizontally and open RIGHT, then LEFT of them !");
open();
rename("R");
open();
rename("L");
print("horizontal:");
run("Pairwise stitching", "first_image=R second_image=L fusion_method=[Linear Blending] fused_image=R<->L check_peaks=5 compute_overlap x=0 y=0 registration_channel_image_1=[Average all channels] registration_channel_image_2=[Average all channels]");
close("R");
close("L");
close("R<->L");	
waitForUser("Identify two tiles adjacent vertically and open BOTTOM, then TOP of them !");
open();
rename("B");
open();
rename("T");
print(" ");
print("vertical:");
run("Pairwise stitching", "first_image=B second_image=T fusion_method=[Linear Blending] fused_image=B<->T check_peaks=5 compute_overlap x=0 y=0 registration_channel_image_1=[Average all channels] registration_channel_image_2=[Average all channels]");
close("B");
close("T");
close("B<->T");
selectWindow("Log");	}

Dialog.create("Stitching setup");
Dialog.addMessage("Use (x,y) numbers listed in the Log");
Dialog.addNumber("Enter x offset for horizontal pair:", 0);
Dialog.addNumber("Enter y offset for horizontal pair:", 0);
Dialog.addNumber("Enter x offset for vertical pair:", 0);
Dialog.addNumber("Enter y offset for vertival pair:", 0);
Dialog.addMessage("Open TILES folder separately and figure out size of the mosaic size");
Dialog.addNumber("How many rows?", 0);
Dialog.addNumber("How many columns?", 0);
Dialog.addCheckbox("Annotate RGB mosaic with its filename", true);
Dialog.addNumber("Length of scale bar in um (none if 0):", 0);
Dialog.show();
ohx=Dialog.getNumber();
ohy=Dialog.getNumber();
ovx=Dialog.getNumber();
ovy=Dialog.getNumber();
rws=Dialog.getNumber();
cls=Dialog.getNumber();
lbl=Dialog.getCheckbox();
scbr=Dialog.getNumber();
print("horizontal offset (x,y): ", ohx, ohy);
print("vertical offset (x,y): ", ovx, ovy);
print("mosaic: ", rws, " rows x ",cls, " columns");
print("filename imprinted onto RGB mosaic:", lbl);	
if(scbr>0) {print("scale bar:", scbr, "um");
	}

if(srt==0) {myDir11 = myDir4+"row_1_bottom"+File.separator;
File.makeDirectory(myDir11);
myDir12 = myDir4+"row_2"+File.separator;
File.makeDirectory(myDir12);
myDir13 = myDir4+"row_3"+File.separator;
File.makeDirectory(myDir13);
myDir14 = myDir4+"row_4"+File.separator;
File.makeDirectory(myDir14);
myDir15 = myDir4+"row_5"+File.separator;
File.makeDirectory(myDir15);
myDir16 = myDir4+"row_6"+File.separator;
File.makeDirectory(myDir16);
myDir17 = myDir4+"row_7"+File.separator;
File.makeDirectory(myDir17);
myDir18 = myDir4+"row_8"+File.separator;
File.makeDirectory(myDir18);
myDir19 = myDir4+"row_9"+File.separator;
File.makeDirectory(myDir19);
myDir20 = myDir4+"row_10"+File.separator;
File.makeDirectory(myDir20);

Dialog.create("Sort tiles into rows");
Dialog.addMessage("Open TILES folder separately and manually sort tiles into corresponding subfolders,\nstarting from the bottom row (Create more folders if needed or delete some, if not !)");
Dialog.addMessage("Then, for each consecutive row (starting with the bottom one), repeat following steps:\n1) Select subfolder containing row's tiles\n2) Separately, open that subfolder for inspection\n   (if needed, make changes to file numbers manually inside the folder to re-oreder them)\n3) Mark choices in the consecutive Dialog Box\n4) Click OK\nOnce loop completes, continue upwards with the next row, etc.");
Dialog.show();	}

if(srt==1)	{waitForUser("Next, follow those steps for each row (starting with the bottom one):\n1) Select subfolder containing row's tiles\n2) Separately, open that subfolder for inspection\n   (if needed, make changes to file numbers manually inside the folder to re-oreder them)\n3) Mark choices in the consecutive Dialog Box\n4) Click OK\nOnce loop completes, continue upwards with the next row, etc.");
	}

if(pdd==0) {newImage("C1-x", "16-bit black", width, height, 1);
	run("Duplicate...", "title=C2-x");
	run("Duplicate...", "title=C3-x");
	run("Merge Channels...", "c1=C1-x c2=C2-x c3=C3-x create");
	rename("extra_b");
	run("Add...", "value=100");
	run("Duplicate...", "title=extra_w duplicate");
	run("Add...", "value=65435");
for (s = 0; s < rws; s++) {j=101+s;
		nxt=getDirectory("Select subfolder containing tiles of single row. Start with the bottom row and continue upwards");
		Dialog.create("Row setup");
		items=newArray("Yes", "No");
		Dialog.addCheckbox("The tiles inside the folder are numbered as expected in the final mosaic, from left to right?", false);
		Dialog.addNumber("How many extra tiles are needed on the LEFT end of this row?", 0);
		Dialog.addNumber("How many extra tiles are needed on the RIGHT end of this row?", 0);
		itemc=newArray("White", "Black");
		Dialog.addChoice("What color is preferred for extra tiles", itemc);
		Dialog.show();
		ord=Dialog.getCheckbox();
		lpd=Dialog.getNumber();
		rpd=Dialog.getNumber();
		bw=Dialog.getChoice();
		print("tile_folder:  ", nxt, "  L-->R orientation?  ", ord, "  extra tiles on the left:  ", lpd, "  extra tiles on the right:  ", rpd, "  color:  ", bw);
	
if(bw=="White") {selectWindow("extra_w");
		run("Duplicate...", "title=extra duplicate");	}
else {selectWindow("extra_b");
		run("Duplicate...", "title=extra duplicate");		}

if(lpd>0) {selectWindow("extra");
			for (i = 0; i < lpd; i++) {if(ord==0) {saveAs("Tiff", nxt+2000+i);
											rename("extra");	}
										else {saveAs("Tiff", nxt+1000+i);
											rename("extra");	}	}	}
if(rpd>0) {selectWindow("extra");
			for (i = 0; i < rpd; i++) {if(ord==0) {saveAs("Tiff", nxt+1000+i);
											rename("extra");	}
										else {saveAs("Tiff", nxt+2000+i);
											rename("extra");	}	}	}
close("extra");
rowlist=getFileList(nxt);
open(nxt+rowlist[0]);
setBatchMode(true);
if(ord==1) {run("Flip Horizontally"); }
rename("R");
for (u = 1; u < rowlist.length; u++) {open(nxt+rowlist[u]);
		if(ord==1) {run("Flip Horizontally"); }
		rename("L");
run("Pairwise stitching", "first_image=R second_image=L fusion_method=[Linear Blending] fused_image=R<->L check_peaks=5 x=ohx y=ohy registration_channel_image_1=[Average all channels] registration_channel_image_2=[Average all channels]");
close("R");
close("L");
rename("R");	}
if(ord==1) {run("Flip Horizontally"); }
saveAs("Tiff", myDir5+"row_"+j);
close();
setBatchMode(false);	}		
close("extra_w");
close("extra_b");	}

if(pdd==1) {
for (s = 0; s < rws; s++) {j=101+s;
		nxt=getDirectory("Select subfolder containing tiles of single row. Start with the bottom row and continue upwards");
			Dialog.create("Setup check");
			Dialog.addCheckbox("Indicate if tiles inside the folder are numbered as expected in the final mosaic, from left to right?", false);
			Dialog.show();
			ord=Dialog.getCheckbox();
			print("  L-->R orientation?  ", ord);
rowlist=getFileList(nxt);
open(nxt+rowlist[0]);
setBatchMode(true);
if(ord==1) {run("Flip Horizontally"); }
rename("R");
for (u = 1; u < rowlist.length; u++) {open(nxt+rowlist[u]);
		if(ord==1) {run("Flip Horizontally"); }
		rename("L");
run("Pairwise stitching", "first_image=R second_image=L fusion_method=[Linear Blending] fused_image=R<->L check_peaks=5 x=ohx y=ohy registration_channel_image_1=[Average all channels] registration_channel_image_2=[Average all channels]");
close("R");
close("L");
rename("R");	}
if(ord==1) {run("Flip Horizontally"); }
saveAs("Tiff", myDir5+"row_"+j);
close();
setBatchMode(false);	}	}

tlist5=getFileList(myDir5);
open(myDir5+tlist5[0]);
rename("B");
for (g = 1; g < tlist5.length; g++) {open(myDir5+tlist5[g]);
rename("T");
run("Pairwise stitching", "first_image=B second_image=T fusion_method=[Linear Blending] fused_image=B<->T check_peaks=5 x=ovx y=ovy registration_channel_image_1=[Average all channels] registration_channel_image_2=[Average all channels]");
close("B");
close("T");
rename("B");	}	

mos=getBoolean("Is assembly correct?", "Yes", "No - start again from sorted tiles (correct sorting/padding manually)");
print(mos);
if(mos==0) {for (h=0; h<tlist5.length; h++)	
ok = File.delete(myDir5+tlist5[h]);
ok = File.delete(myDir5);
close();
print("aborted");
selectWindow("Log");
saveAs("Text", output+"Log"+"_"+month+"_"+dayOfMonth+"_"+year+"_"+hour+"_"+minute+".txt");
close("Log");
 }	

if(mos==1) {crp=getBoolean("Do you want to crop this mosaic");
if(crp==1) {setTool("rectangle");
waitForUser("Select cropping area");
run("Crop");	}
saveAs("Tiff", output+"mosaic_"+ttl);
if(mscs==1) {saveAs("Tiff", mosaics+"mosaic_"+ttl);
	}

Dialog.create("Gamma adjustment");
items=newArray("No", "Quite dark", "Very dark");
Dialog.addRadioButtonGroup("Is the slice too dark?", items, 3, 1, "No");
Dialog.show();
gm=Dialog.getRadioButton();
if(gm=="No") {gmma=1;	}
if(gm=="Quite dark") {gmma=0.5;	}
if(gm=="Very dark") {gmma=0.3;	}
rename("x");
waitForUser("Select a representative background area");
setBatchMode(true);
run("Duplicate...", "duplicate");
rename("y");
run("Split Channels");
selectWindow("C1-y");
run("Measure");
bck1=getResult("Mean");
selectWindow("C2-y");
run("Measure");
bck2=getResult("Mean");
selectWindow("C3-y");
run("Measure");
bck3=getResult("Mean");
close("Results");
close("C1-y");
close("C2-y");
close("C3-y");
run("Select None");
run("Split Channels");

selectWindow("C1-x");
run("Enhance Contrast", "saturated=0.35");
getMinAndMax(min, max);
mir=min;
setMinAndMax(mir, bck1);
run("Gamma...", "value=gmma");
selectWindow("C2-x");
run("Enhance Contrast", "saturated=0.35");
getMinAndMax(min, max);
mig=min;
setMinAndMax(mig, bck2);
run("Gamma...", "value=gmma");
selectWindow("C3-x");
run("Enhance Contrast", "saturated=0.35");
getMinAndMax(min, max);
mib=min;
setMinAndMax(mib, bck3);
run("Gamma...", "value=gmma");
run("Merge Channels...", "c1=C1-x c2=C2-x c3=C3-x create");
run("RGB Color");
rename("rgb");
close("x");
getDimensions(width, height, channels, slices, frames);
fntsz=height/40;
if(scbr>0) {run("Scale Bar...", "width=scbr height=20 font=fntsz color=Black background=None location=[Upper Right] bold overlay");
run("Flatten");
	}
else {run("Duplicate...", " ");	}
rename(ttl);
run("Images to Stack", "name=Stack title=[] use");
if(lbl==1) {run("Make Montage...", "columns=1 rows=1 first=2 last=2 scale=1 font=fntsz label");		}
else {run("Make Montage...", "columns=1 rows=1 first=2 last=2 scale=1 font=fntsz");		}
close("Stack");
saveAs("Tiff", output+ttl+"_RGB_mosaic");
if(mscs==1) {saveAs("Tiff", mosaics+ttl+"_RGB_mosaic");	}

print("Gamma=", gmma);



close();
for (h=0; h<tlist5.length; h++)	
ok = File.delete(myDir5+tlist5[h]);
ok = File.delete(myDir5);

selectWindow("Log");
saveAs("Text", output+"Log"+"_"+ttl+"_"+month+"_"+dayOfMonth+"_"+year+"_"+hour+"_"+minute+".txt");
	}
close("Log");
}


if(prc==1) {setTool("rectangle");
run("Set Measurements...", "area mean min integrated median display scientific redirect=None decimal=0");
mosrgb=getDirectory("Select Folder to store RGB versions of mosaics");
mosaics=getDirectory("Select Folder containing assembled mosaics");
print("source: ", mosaics);
print("results: ", mosrgb);
Dialog.create("Mosaic setup");
Dialog.addCheckbox("Annotate RGB mosaic with its filename", true);
Dialog.addNumber("Length of scale bar in um (none if 0):", 0);
Dialog.show();
lbl=Dialog.getCheckbox();
scbr=Dialog.getNumber();
if(lbl==1) {print("filename imprinted onto RGB mosaic:", lbl);	}
if(scbr>0) {print("scale bar:", scbr, "um");	}
print("");

NAMES=getFileList(mosaics);

for (i=0; i<NAMES.length; i++) {open(mosaics+NAMES[i]);
ttl=File.nameWithoutExtension;
rename("x");
getDimensions(width, height, channels, slices, frames);

Dialog.create("Gamma adjustment");
items=newArray("No", "Quite dark", "Very dark");
Dialog.addRadioButtonGroup("Is the slice too dark?", items, 3, 1, "No");
Dialog.show();
gm=Dialog.getRadioButton();
if(gm=="No") {gmma=1;	}
if(gm=="Quite dark") {gmma=0.5;	}
if(gm=="Very dark") {gmma=0.3;	}

waitForUser("Select a representative background area");
setBatchMode(true);
run("Duplicate...", "duplicate");
rename("y");
run("Split Channels");
selectWindow("C1-y");
run("Measure");
bck1=getResult("Mean");
selectWindow("C2-y");
run("Measure");
bck2=getResult("Mean");
selectWindow("C3-y");
run("Measure");
bck3=getResult("Mean");
close("Results");
close("C1-y");
close("C2-y");
close("C3-y");

run("Select None");
run("Split Channels");

selectWindow("C1-x");
run("Enhance Contrast", "saturated=0.35");
getMinAndMax(min, max);
vmin1=min;
setMinAndMax(vmin1, bck1);
run("Gamma...", "value=gmma");

selectWindow("C2-x");
run("Enhance Contrast", "saturated=0.35");
getMinAndMax(min, max);
vmin2=min;
setMinAndMax(vmin2, bck2);
run("Gamma...", "value=gmma");

selectWindow("C3-x");
run("Enhance Contrast", "saturated=0.35");
getMinAndMax(min, max);
vmin3=min;
setMinAndMax(vmin3, bck3);
run("Gamma...", "value=gmma");

print(ttl);
print("Red:   ", "white=", bck1, "   black=", vmin1);
print("Green:   ", "white=", bck2, "   black=", vmin2);
print("Blue:", "white=", bck3, "   black=", vmin3);
print("Gamma=", gmma);


fntsz=height/40;

run("Merge Channels...", "c1=C1-x c2=C2-x c3=C3-x create");
run("RGB Color");
rename("rgb");
close("x");
if(scbr>0) {run("Scale Bar...", "width=scbr height=20 font=fntsz color=Black background=None location=[Upper Right] bold overlay");
run("Flatten");	}
else {run("Duplicate...", " ");	}
rename(ttl);
run("Images to Stack", "name=Stack title=[] use");
if(lbl==1) {run("Make Montage...", "columns=1 rows=1 first=2 last=2 scale=1 font=fntsz label");
	}
else {run("Make Montage...", "columns=1 rows=1 first=2 last=2 scale=1 font=fntsz");		}
close("Stack");
saveAs("Tiff", mosaics+ttl+"_RGB_mosaic");
close();
setBatchMode(false);
print("");
	 }	

selectWindow("Log");
saveAs("Text", mosaics+"Log"+"_"+ttl+"_"+month+"_"+dayOfMonth+"_"+year+"_"+hour+"_"+minute+".txt");
close("Log");	}