We just fixed a related bug, #805. Can you please update your Fiji and test again? Hopefully Fiji will now actually quit when you quit the program, and your macro will terminate.

The Kill button being grayed out is a separate issue, which is why this bug report is not a duplicate of 805.

Hello,

this bug is be back, but not with all macros.
The macro who bug is just a macro with "analyze particles" and "save results".
And macro occupies more memory to each loop. 

You have an idea to fix this?
Thank you in advance. 
best regards, 
Quentin

> The macro who bug is just a macro with "analyze particles" and "save results".

I can not reproduce this by running analyze particles and saving the results. You said that your macro runs a loop so I am wondering if the loop is not terminating, or running a significant number of times and the UI is just not updating properly.

Can you please share the exact contents of your macro?

> And macro occupies more memory to each loop.

Assuming you are opening multiple datasets in your loop and then calling close(), there is at least one known memory leak. See http://fiji.sc/bugzilla/﷒0﷓ and related discussion.

827 comments bug helped me and the solution is indeed uncheck "Use SCIFIO When opening files". macro becomes much faster and occupies only the memory that is required. 

Thank you very much for your help. 
Quentin

Quentin,

> the solution is indeed uncheck "Use SCIFIO When opening files"

This is a quick fix but not a true solution. It does not address the underlying bug that you discovered. You can read more about ImageJ2 and SCIFIO here: http://imagej.net/ImageJ2

There is clearly still a bug on the SCIFIO/ImageJ2 side of things, and it will need to be resolved eventually. So it would be very helpful if you would post your macro code so we can test, reproduce and fix the issue (and of course you can continue to run without using SCIFIO until the problem is resolved).

Thanks,
Mark

My entire project uses two macro. The first was running perfectly smoothly and continuously. The second was blocking and now execute perfectly.

MACRO 1:

dossierOut_2 = getDirectory("Dossier pour les images avec les segmentations");
//Dossier enregistrement de la segmentations

setBatchMode(true);
x=1

		//chemin d'access
		path = "C:\\Users\\Quentin\\Desktop\\Images Zeiss + macros\\dossier 1_ stock image\\J2 1Fe 3x3 20x R1P2.zvi";
				for (i=50; i>=5; i-=5)
				{
					for (j=200; j>=0; j-=10)
					{
						for (k=200; k>=0; k-=10)
						{	
						//importation des fichiers ZIV, séparation des tuilles
						run("Bio-Formats Importer", 
						"open=path autoscale color_mode=Default view=Hyperstack stack_order=XYCZT series_2");
						NOMx=getTitle();
						
						//duplicat
						run("Duplicate...", "title="+NOMx+"_"+i+" duplicate range=1-7");
						NOMx_1= getTitle();
				
						//stack focuser (EFI)
						run("Stack Focuser ", "enter="+i);
										
						//run("Brightness/Contrast...");			
						setMinAndMax(j, 4095);
						run("8-bit");
						
						
						//treshold pour la segmentation
						setAutoThreshold("Yen dark");
						setThreshold(k, 4095);
						run("Convert to Mask");
				
						saveAs("Tiff", dossierOut_2+NOMx_1+"_"+i+"_"+j+"_"+k+".tif");
						close();
						close();
						close();

						//Fenetre_mémoire
						print("traitement ",x,"sur 4410  ",IJ.freeMemory());
						x=x+1;
						
						}			
						
					}
				}
						
		print("...");
		print("traitement accompli");
		print("...");

................................................................................
................................................................................

MACRO 2:

dossierIn = getDirectory("Images"); //Dossier dans lequel les photos sont
dossierOut = getDirectory("Excel"); //Dossier dans lequel les données sont enregistrées
fichiers = getFileList(dossierIn);
setBatchMode(true);

	for (Z=0; Z<fichiers.length; Z++)
	{
				
		open(dossierIn+fichiers[Z]);
		run("Analyze Particles...", "size=40-Infinity display exclude");

			if (isOpen("Results")) 
			{ 
		       selectWindow("Results");
		       saveAs("Results", dossierOut+fichiers[Z]+"_Results.txt");
		       run("Clear Results");
		       run("Close"); 
		  	}

		  	if (isOpen("ROI Manager")) 
			{ 
		       selectWindow("ROI Manager");
		       run("Close"); 
		  	}
			
		close();
		//Fenetre_d'avancement
		print(Z+1 +"/"+fichiers.length+"     "+IJ.freeMemory());
	}
		print("...");
		print("traitement accompli");
		print("...");

Thanks for this, Quentin. We'll look into it.

Hello, just a little question: if I find a new "bug" I make a new post ?
thanks,
Quentin

Yep, one bug per post. The easiest way is to use Help > Report a Bug from within Fiji.

See also http://fiji.sc/Bug_reporting_best_practices