/*
Author: Ahsen Chaudhry
Last updated: April 27, 2022
This macro will add each mitochondrial object in 2D slices to the ROI manager. The assigned number labels to the mitochondria 
correspond to the results of the 2D Analysis command.
*/

macro Display2DMitoROI
{
	inputName = getTitle();
		isThresholded = false;
		getHistogram(values,counts,256);
		counter = 0;
		for (i = 0; i < values.length; i++) {if (counts[i]>1) counter++;}
		if (counter<=2) isThresholded = true;
		if (isThresholded==false) exit("Needs a thresholded input");
	
	var mitoCount;
	run("ROI Manager...");
	setBatchMode(true);
	sizeFilter = 0.06;//microns^2
	
	run("Invert LUT");
	run("Set Measurements...", "area perimeter shape redirect=None decimal=3");
	run("Analyze Particles...", "size="+sizeFilter+"-Infinity show=[Count Masks] display clear");
	selectWindow(inputName);
	run("Invert LUT");
	mitoCount = Table.size("Results");
	close("Results");
	for (i = 0; i < mitoCount;i++)
	{
		selectWindow("Count Masks of " + inputName);
		run("Duplicate...", "duplicate");
		rename(inputName + "$t$");
		setThreshold(i+1, i+1);
		run("Convert to Mask", "method=Default background=Dark black");
		run("8-bit");
		run("Create Selection");
		//run("Make Inverse");
		selectWindow(inputName);
		run("Restore Selection");
		roiManager("add");	
		roiManager("select", roiManager("count")-1);			
		roiManager("rename", "Mito# " + (i+1));
		selectWindow(inputName + "$t$");
		close(inputName + "$t$");
	}
	close("Count Masks of " + inputName);
	setBatchMode(false);
	selectWindow(inputName);
}