Laboratoire RDP » Biophysics Team » FLORIVAR

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//The script will process all your .inr.gz files in the chosen folder.

//The stacks will be saved in subfolders named as the treated lif files.

print ("===========================");

print ("==== Macro inr2tif.ijm ====");

//Choose the directory containing your .inr.gz files//

dir = getDirectory("Choose a directory")

setBatchMode(true);

list = getFileList(dir);

print(dir);

ShortNameDir=substring(dir,0,lastIndexOf(dir,"/"));

print (ShortNameDir);

dirout=ShortNameDir+"-tif/";

print("Creating output directory ",dirout);

File.makeDirectory(dirout);

for (FileInd=0; FileInd<list.length; FileInd++){

	FileName = list[FileInd];

	if(endsWith (FileName, ".inr.gz")){

		print ("### Processing ",FileName," ###");

		path = dir+FileName;

		ShortName=substring(FileName,0,indexOf(FileName,".inr.gz"));

		run("Bio-Formats Importer", "open=["+path+"] color_mode=Default view=Hyperstack stack_order=XYCZT use_virtual_stack open_all_series ");

		TiffName=ShortName+".tif";

		saveAs("Tiff", dirout+TiffName);

		run("Close All");

		print("Done with", FileName,"!");

	} else {

	print("### ",FileName," Not an .inr.gz file ###");

	};

};	

print("Done with this folder!!!");