// Script import oif files, make z projection and save it in new "Z_projection", located in the original folder as tiffs.

run("Close All");

dir = getDirectory("Choose Source Directory ");
list = getFileList(dir);
Array.sort(list);

fs=File.separator;
pathStore=dir;
savePath=pathStore+fs+"Tiffs";
File.makeDirectory(savePath);


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

    // select only oif type files
    if(endsWith(list[i],"czi")){
    	
   
     fileName = dir + list[i];
     
     // import image
     run("Bio-Formats", "open=["+fileName+"] + autoscale color_mode=Default view=Hyperstack stack_order=XYCZT");
     imTitle = getTitle();

         
     newTitle = getTitle(); 
     newTitle = replace(newTitle, ".oif", "");       

     //save as tiff
     saveAs("Tiff", savePath+fs+newTitle+".tif");

     close(imTitle);
    
    };

	
};