_DKR_Straighten_Spindle.txt

//ImageJ macro
//20090617
//made by Dan Rozelle
//
//macro made when I was trying to compare recruitment of fluorescent motors on the anaphse spindle.
//this macro takes a folder of projected spindles as input and creates an image for each projection
//where the spindle is straightened and positioned horizontally
//essentially this automates the "Deconvolution>Straighten to Line" plugin 
//
//this also places the pixel values of the spindle from this horizontal line into a results table
//which can then be manipulated in excel, etc...



macro "_DKR_Straighten_Spindle" {


dir1 = getDirectory("Choose source directory");
if (dir1=="")
      exit("No directory available");

//get a list of all the files in this folder 
list = getFileList(dir1);

// Create a results directory in dir1
  dir2 = dir1+"Linearized Spindles"+File.separator;
  File.makeDirectory(dir2);
  if (!File.exists(dir2))
      exit("Unable to create directory");


for(i=0;i<list.length;i++){
	
	open(dir1+list[i]);
	
selectWindow(list[i]);
Stack.getDimensions(width, height, channels, slices, frames);

//get rid of the second channel if present
if(channels > 1) {
	run("Stack to Images");
	nameext = list[i];
	name = substring(nameext,0,lengthOf(nameext)-4);
	
	selectWindow(name+"-0002");
	close();
	selectWindow(name+"-0001");
	rename(list[i]);
	}

//prepare image for straightening, start the straighten plugin 
selectWindow(list[i]);
run("Grays");
run("Enhance Contrast", "saturated=0.5");
//once you convert to 32-bit, DO NOT CONVERT BACK TO 16-BIT, 
//ImageJ opens DV files as 16-bit signed int, but conversion back will give 16-bit unsigned int...very different
run("32-bit");
run("Straighten to Line");
run("Set... ", "zoom=400");
setLocation(200,0);

//close original image
selectWindow(list[i]);
close();

//user draws a segmented line to be straightened, clicks the straighten line, and then proceeds
waitForUser("straighten the spindle and close the plugin window");
selectWindow("Straighten: "+list[i]);
close();

//rename straightened image
selectWindow("(1) Straightened Filament ");

run("Properties...", "unit=micron pixel_width=0.1121460 pixel_height=0.1121460 ");
savename = "spdl_"+list[i];
saveAs("Tiff", dir2+savename);

//append pixel veasurements to results table
	getDimensions(width, height, channels, slices, frames);
	getPixelSize(unit, pixelWidth, pixelHeight);
	spindleLength = width*pixelWidth;
	
	//add more lines in the results table if it is not long enough
	for(line=0;line<width;line++){
		setResult(unit,line,line*pixelWidth);
		}
	//append the data to a new labeled column
	for(line=0;line<width;line++){
		value = (getPixel(line,height/2))-32768;
		setResult(savename,line,value);
		}
	
	updateResults();
	selectWindow(savename);
	close();

}

}