Extract multi-series file and resave as TIFF stacks or slices #Fiji #ImageJ #Macro #BIOP

Export_Images_Folder.ijm

/*
 * Complex Format EXPORT MACRO
 * By Olivier Burri @ EPFL - SV - PTECH - BIOP
 * Given a folder, extracts all series inside all multi-file files with given extension in new folders 
 * Last edit: 13.02.2017
 */


 ////////////////////// SET PARAMETERS //////////////////////
 ////////////////////////////////////////////////////////////
 
 
// Set the extension you would like this macro to work with.
// Do not add a . at the beggining
extension = "czi";  //eg "lif", "vsi", etc...


// Set to true if you want all planes of the image to be saved individually
// if set to false, it will save each series as a stack. 
is_save_individual_planes = true; // set to either true or false

// Padding for the naming of the series if you want to save all 
// Images individually
pad = 3; // 0 means no padding. 2 means '01', '02' etc...


 //////////////////// END SET PARAMETERS ////////////////////
 ////////////////////////////////////////////////////////////
 




// Beggining of macro. You should now have anything to edit after this line. 

dir = getDirectory("Select a directory containing one or several ."+extension+" files.");

files = getFileList(dir);


setBatchMode(true);
k=0;
n=0;

run("Bio-Formats Macro Extensions");
for(f=0; f<files.length; f++) {
	if(endsWith(files[f], "."+extension)) {
		k++;
		id = dir+files[f];
		Ext.setId(id);
		Ext.getSeriesCount(seriesCount);
		print(seriesCount+" series in "+id);
		n+=seriesCount;
		for (i=0; i<seriesCount; i++) {
			run("Bio-Formats Importer", "open=["+id+"] color_mode=Default view=Hyperstack stack_order=XYCZT series_"+(i+1));
			fullName	= getTitle();
			dirName 	= substring(fullName, 0,lastIndexOf(fullName, "."+extension));
			fileName 	= substring(fullName, lastIndexOf(fullName, " - ")+3, lengthOf(fullName));
			File.makeDirectory(dir+File.separator+dirName+File.separator);

			print("Saving "+fileName+" under "+dir+File.separator+dirName);
			
			getDimensions(x,y,c,z,t);
			
			
			if(is_save_individual_planes) {
				save_string = getSaveString(pad);
				print(dir+File.separator+dirName+File.separator+fileName+"_"+save_string+".tif");
				run("Image Sequence... ", "format=TIFF name=["+fileName+"] digits="+pad+" save=["+dir+File.separator+dirName+File.separator+"]");
				
			} else {
				saveAs("tiff", dir+File.separator+dirName+File.separator+fileName+"_"+(i+1)+".tif");
			}
			run("Close All");
		}
	}
}
Ext.close();
setBatchMode(false);
showMessage("Done with "+k+" files and "+n+" series!");


function getSaveString(pad) {
	str ="";
	getDimensions(x,y,c,z,t);
	if(t > 1)  str+="t_"+IJ.pad(1,pad);
	if(z > 1)  str+="z_"+IJ.pad(1,pad);
	if(c > 1)  str+="c_"+IJ.pad(1,pad);
	
	return str;
}

Is it possible to do split channels with this script? I tried added that option to the script but it messed up the file names.

Hello!

Thank you so much for making this script! It has helped me tremendously in processing large datasets. I recently updated FIJI to the newest version, and am now getting an error. I was wondering if you can help me address this?

Specifically in line 54:
dirName = substring(fullName, 0,lastIndexOf(fullName, "."+extension));

I am now getting this error message attached below, with the following debug window. I am using ImageJ version 2.14.0/1.54f Build: c89e8500e4

perhaps you put a dot when specifying the extension? or the image is the wrong extension?

@lacan I appreciate that you are still active on this post!

I was just able to find the issue when manually saving at tifs last night, my .lif file name was too long and it created ellipsis! I guess FIJI does have a character limit for file naming. I was able to get it running after making the file name shorter. Good to know!

good to know. the ellipsis might me talked to a Mac file path issue, as Fiji is just reading the filename in the macro. thanks for the report!