root / bin / ImageJ / lif2tif.ijm @ 18
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| 1 | 1 | akiss | ////////////////////////////////////////////////////////////////////////////////// |
|---|---|---|---|
| 2 | 1 | akiss | |
| 3 | 1 | akiss | //The script will process all your .lif files in the chosen folder. |
| 4 | 1 | akiss | //The stacks will be saved in subfolders named as the treated lif files. |
| 5 | 1 | akiss | |
| 6 | 1 | akiss | print ("====================================");
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| 7 | 1 | akiss | print ("======== Macro lif2tif.ijm =========");
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| 8 | 1 | akiss | print ("====================================");
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| 9 | 1 | akiss | |
| 10 | 1 | akiss | //Choose the directory containing your .lif file// |
| 11 | 1 | akiss | dir = getDirectory("Choose a directory")
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| 12 | 1 | akiss | setBatchMode(true); |
| 13 | 1 | akiss | list = getFileList(dir); |
| 14 | 1 | akiss | |
| 15 | 1 | akiss | //Find .lif experiment// |
| 16 | 1 | akiss | for (FileInd=0; FileInd<list.length; FileInd++){
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| 17 | 1 | akiss | FileName = list[FileInd]; |
| 18 | 1 | akiss | if(endsWith (FileName, "lif")){
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| 19 | 1 | akiss | print ("### Processing ",FileName," ###");
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| 20 | 1 | akiss | path = dir+FileName; |
| 21 | 1 | akiss | ShortName=substring(FileName,0,indexOf(FileName,".lif")); |
| 22 | 1 | akiss | print("Creating output directory ",ShortName);
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| 23 | 1 | akiss | File.makeDirectory(dir+ShortName); |
| 24 | 1 | akiss | //Open .lif// |
| 25 | 1 | akiss | run("Bio-Formats Importer", "open=["+path+"] color_mode=Default view=Hyperstack stack_order=XYCZT use_virtual_stack open_all_series ");
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| 26 | 1 | akiss | //Saving as .tif the content of the .lif files, in their destination folders// |
| 27 | 1 | akiss | list = getList("image.titles");
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| 28 | 1 | akiss | //get the name of each image opened// |
| 29 | 1 | akiss | ids=newArray(nImages); |
| 30 | 1 | akiss | for (j=0; j<list.length; j++){
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| 31 | 1 | akiss | //print(list[j]); |
| 32 | 1 | akiss | selectImage(j+1); |
| 33 | 1 | akiss | ids[j]=getTitle; |
| 34 | 1 | akiss | //Get experiment name (title of the .lif file)// |
| 35 | 1 | akiss | experiment_name=substring(ids[j],0,indexOf(ids[j],".lif")); |
| 36 | 1 | akiss | //Remove the name of the .lif file that is included in each image// |
| 37 | 1 | akiss | short_name1 = substring(ids[j], indexOf(ids[j], "- "), lastIndexOf(ids[j], "")); |
| 38 | 1 | akiss | short_name = replace(short_name1, "- ", ""); |
| 39 | 1 | akiss | //If not a stack, save directly as .tif with a short name// |
| 40 | 1 | akiss | if (nSlices==1){
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| 41 | 1 | akiss | print("Not a stack");
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| 42 | 1 | akiss | run("8-bit");
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| 43 | 1 | akiss | saveAs("Tiff", dir+File.separator+experiment_name+File.separator+short_name);
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| 44 | 1 | akiss | print(short_name, ">>> Image saved as .tif"); |
| 45 | 1 | akiss | //If a stack, reverse and save as .tif with a short name// |
| 46 | 1 | akiss | } else {
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| 47 | 1 | akiss | run("Reverse");
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| 48 | 1 | akiss | run("8-bit");
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| 49 | 1 | akiss | saveAs("Tiff", dir+File.separator+experiment_name+File.separator+short_name);
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| 50 | 1 | akiss | print("----- ",short_name, " >>> Reversed and saved as .tif");
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| 51 | 1 | akiss | }; |
| 52 | 1 | akiss | getPixelSize(unit, pw, ph, pd); |
| 53 | 1 | akiss | print("Voxelsize="+pw+"x"+ph+"x"+pd+" "+unit+"^3");
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| 54 | 1 | akiss | print("nSlices="+nSlices);
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| 55 | 1 | akiss | }; |
| 56 | 1 | akiss | run("Close All");
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| 57 | 1 | akiss | print("Done with", FileName,"!");
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| 58 | 1 | akiss | } else {
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| 59 | 1 | akiss | print("### ",FileName," Not a .lif file###");
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| 60 | 1 | akiss | }; |
| 61 | 1 | akiss | }; |
| 62 | 1 | akiss | print("Done with this folder!!!");
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| 63 | 1 | akiss | |
| 64 | 1 | akiss | |
| 65 | 1 | akiss |