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/**
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* MRI Image Conversion Tools
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* Tools for batch-converting lsm or lif images to tif
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*
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* Work on a folder containing lif or lsm files
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* For each file and for each image it contains:
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* - save the channels each as a tif file
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* - save the overlay as an RGB tif file
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* - optional: save stacks as projections
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*
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* written 2011 by Volker Baecker (INSERM) at Montpellier RIO Imaging (www.mri.cnrs.fr)
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*
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* The Lif2Tif macro is based on the Leica LIF Extractor macro by Christophe LETERRIER (http://christopheleterrier.com/LeterrierSOFT.html)
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* which is based on the ZStacks Projector macro version 1.1 14/05/2008
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*/
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var helpURL = "http://dev.mri.cnrs.fr/wiki/imagej-macros/Image_Conversion_Tools"
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var DO_PROJECTION = false;
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var USE_ALL_SLICES_FOR_PROJECTION = false;
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var PROJECTION_START_SLICE = 1;
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var PROJECTION_END_SLICE = 3;
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var PROJECTION_METHOD = "Max Intensity";
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var CHANNELS_STRING = "1111";
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var OUTPUT_SUBFOLDER = "tif"
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macro "Unused Tool - C037" { }
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macro "MRI Image Conversion Tools Help Action Tool - C000T4b12?" {
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run('URL...', 'url='+helpURL);
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}
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macro "Lif2Tif Action Tool - C037T0b11LT7b09iTcb09f" {
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DIR_PATH=getDirectory("Select a directory");
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OUTPUT_DIR = DIR_PATH + "/" + OUTPUT_SUBFOLDER;
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File.makeDirectory(OUTPUT_DIR);
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print("\\Clear");
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print("converting lif file in folder: "+DIR_PATH);
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// Get all file names
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ALL_NAMES=getFileList(DIR_PATH);
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ALL_EXT=newArray(ALL_NAMES.length);
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// Create extensions array
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for (i=0; i<ALL_NAMES.length; i++) {
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LENGTH=lengthOf(ALL_NAMES[i]);
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ALL_EXT[i]=substring(ALL_NAMES[i],LENGTH-4,LENGTH);
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}
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setBatchMode(true);
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// Loop on all .lei and .lif extensions
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fileIndex = 0;
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numberOfLifFiles = 0;
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for (n=0; n<ALL_EXT.length; n++) {
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if (ALL_EXT[n]==".lei" || ALL_EXT[n]==".lif") numberOfLifFiles++;
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}
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for (n=0; n<ALL_EXT.length; n++) {
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if (ALL_EXT[n]==".lei" || ALL_EXT[n]==".lif") {
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fileIndex++;
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// Get the file path
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FILE_PATH=DIR_PATH+ALL_NAMES[n];
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FILE_NAME=File.getName(FILE_PATH);
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// Start BioFormats and get series number in file.
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run("Bio-Formats Macro Extensions");
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Ext.setId(FILE_PATH);
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Ext.getSeriesCount(SERIES_COUNT);
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SERIES_NAMES=newArray(SERIES_COUNT);
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seriesIndex = 0;
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for (i=0; i<SERIES_COUNT; i++) {
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seriesIndex++;
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print("\\Update2:converting image " + (fileIndex) + " of " + numberOfLifFiles + " / series " + seriesIndex + " of " + SERIES_COUNT);
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Ext.setSeries(i);
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Ext.getEffectiveSizeC(CHANNEL_COUNT);
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Ext.getSizeZ(SLICE_COUNT);
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SERIES_NAMES[i]="";
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Ext.getSeriesName(SERIES_NAMES[i]);
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TEMP_NAME=toLowerCase(SERIES_NAMES[i]);
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run("Bio-Formats Importer", "open=["+ FILE_PATH + "] " + " color_mode=Default view=Hyperstack" + " stack_order=Default " + "series_"+d2s(i+1,0));
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Stack.setDisplayMode("composite");
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title = getTitle();
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Stack.setActiveChannels(CHANNELS_STRING);
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run("Stack to RGB", "slices keep");
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rename(title + "-1");
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if (SLICE_COUNT>1 && DO_PROJECTION) doProjection();
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currentTitle = getTitle();
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index = lastIndexOf(currentTitle, ".lif - ");
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name = substring(currentTitle, index+7, lengthOf(currentTitle)-2);
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save(OUTPUT_DIR + "/" + name + " - RGB.tif");
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close();
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run("Split Channels");
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// Loop on each channel (each opened window)
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for(j=1; j<CHANNEL_COUNT+1; j++) {
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selectImage("C"+j+"-"+title);
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if (SLICE_COUNT>1 && DO_PROJECTION) doProjection();
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currentTitle = getTitle();
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index = lastIndexOf(currentTitle, ".lif - ");
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name = substring(currentTitle, index+7, lengthOf(currentTitle));
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save(OUTPUT_DIR + "/" + name + " - C" + j + ".tif");
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close();
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}
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}
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}
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}
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setBatchMode("exit and display");
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showStatus("finished converting lif to tif");
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print("finished converting lif to tif");
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}
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macro "Lsm2Tif Action Tool - C037T0b11LT7b09sTcb09m" {
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DIR_PATH=getDirectory("Select a directory");
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OUTPUT_DIR = DIR_PATH + "/" + OUTPUT_SUBFOLDER;
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File.makeDirectory(OUTPUT_DIR);
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print("\\Clear");
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print("converting lsm file in folder: "+DIR_PATH);
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// Get all file names
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ALL_NAMES=getFileList(DIR_PATH);
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ALL_EXT=newArray(ALL_NAMES.length);
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// Create extensions array
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for (i=0; i<ALL_NAMES.length; i++) {
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LENGTH=lengthOf(ALL_NAMES[i]);
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ALL_EXT[i]=substring(ALL_NAMES[i],LENGTH-4,LENGTH);
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}
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setBatchMode(true);
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// Loop on all .lei and .lsm extensions
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fileIndex = 0;
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numberOfLifFiles = 0;
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for (n=0; n<ALL_EXT.length; n++) {
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if (ALL_EXT[n]==".lsm" ) numberOfLifFiles++;
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}
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for (n=0; n<ALL_EXT.length; n++) {
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if (ALL_EXT[n]==".lsm") {
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fileIndex++;
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// Get the file path
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FILE_PATH=DIR_PATH+ALL_NAMES[n];
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FILE_NAME=File.getName(FILE_PATH);
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print("\\Update2:converting image " + (fileIndex) + " of " + numberOfLifFiles);
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open(FILE_PATH);
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Stack.setDisplayMode("composite");
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title = getTitle();
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getDimensions(width, height, colors, slices, frames);
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SLICE_COUNT = slices;
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Stack.setActiveChannels(CHANNELS_STRING);
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run("Stack to RGB", "slices keep");
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rename(title + "-1");
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if (slices>1 && DO_PROJECTION) doProjection();
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currentTitle = getTitle();
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name = substring(currentTitle, 0, lengthOf(currentTitle)-6);
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save(OUTPUT_DIR + "/" + name + " - RGB.tif");
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close();
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run("Split Channels");
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// Loop on each channel (each opened window)
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for(j=1; j<colors+1; j++) {
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selectImage("C"+j+"-"+title);
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if (slices>1 && DO_PROJECTION) doProjection();
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currentTitle = getTitle();
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name = substring(currentTitle, 3, lengthOf(currentTitle)-4);
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save(OUTPUT_DIR + "/" + name + " - C" + j + ".tif");
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close();
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}
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close();
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}
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}
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setBatchMode("exit and display");
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showStatus("finished converting lsm to tif");
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print("finished converting lsm to tif");
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}
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macro "Zvi2Tif Action Tool - C037T0b11ZT7b09vTcb09i" {
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DIR_PATH=getDirectory("Select a directory");
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OUTPUT_DIR = DIR_PATH + "/" + OUTPUT_SUBFOLDER;
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File.makeDirectory(OUTPUT_DIR);
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print("\\Clear");
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print("converting zvi file in folder: "+DIR_PATH);
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// Get all file names
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ALL_NAMES=getFileList(DIR_PATH);
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ALL_EXT=newArray(ALL_NAMES.length);
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// Create extensions array
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for (i=0; i<ALL_NAMES.length; i++) {
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LENGTH=lengthOf(ALL_NAMES[i]);
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ALL_EXT[i]=substring(ALL_NAMES[i],LENGTH-4,LENGTH);
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}
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setBatchMode(true);
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// Loop on all .lei and .lsm extensions
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fileIndex = 0;
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numberOfLifFiles = 0;
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for (n=0; n<ALL_EXT.length; n++) {
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if (ALL_EXT[n]==".zvi" ) numberOfLifFiles++;
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}
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for (n=0; n<ALL_EXT.length; n++) {
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if (ALL_EXT[n]==".zvi") {
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fileIndex++;
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// Get the file path
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FILE_PATH=DIR_PATH+ALL_NAMES[n];
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FILE_NAME=File.getName(FILE_PATH);
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print("\\Update2:converting image " + (fileIndex) + " of " + numberOfLifFiles);
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run("Bio-Formats Importer", "open=["+FILE_PATH+"] open=["+FILE_PATH+"] autoscale color_mode=Composite view=Hyperstack stack_order=XYCZT");
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Stack.setDisplayMode("composite");
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title = getTitle();
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getDimensions(width, height, colors, slices, frames);
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SLICE_COUNT = slices;
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run("Bio-Formats Macro Extensions");
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Ext.setId(FILE_PATH);
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for (j=1; j<colors+1; j++) {
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Ext.getMetadataValue("MultiChannel Color "+(j-1), colorCode);
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colorCode = parseInt(colorCode,10);
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Stack.setChannel(j);
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blueColor = (colorCode&0xff0000)>> 16;
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greenColor = (colorCode & 0xff00)>>8;
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redColor = colorCode&0xff;
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reds = newArray(256);
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greens = newArray(256);
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blues = newArray(256);
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for (i=0; i<256; i++) {
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reds[i] = round((i / 255.0) * redColor);
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greens[i] = round((i / 255.0) * greenColor);
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blues[i] = round((i / 255.0) * blueColor);
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}
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setLut(reds,greens,blues);
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}
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Stack.setChannel(1);
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Stack.setActiveChannels(CHANNELS_STRING);
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run("Stack to RGB", "slices keep");
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rename(title + "-1");
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if (slices>1 && DO_PROJECTION) doProjection();
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currentTitle = getTitle();
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name = substring(currentTitle, 0, lengthOf(currentTitle)-6);
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save(OUTPUT_DIR + "/" + name + " - RGB.tif");
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close();
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run("Split Channels");
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// Loop on each channel (each opened window)
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for(j=1; j<colors+1; j++) {
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selectImage("C"+j+"-"+title);
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if (slices>1 && DO_PROJECTION) doProjection();
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currentTitle = getTitle();
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name = substring(currentTitle, 3, lengthOf(currentTitle)-4);
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save(OUTPUT_DIR + "/" + name + " - C" + j + ".tif");
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close();
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}
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}
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}
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setBatchMode("exit and display");
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showStatus("finished converting zvi to tif");
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print("finished converting zvi to tif");
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}
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function doProjection() {
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currentTitle = getTitle();
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startSlice = PROJECTION_START_SLICE;
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endSlice = PROJECTION_END_SLICE;
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if (USE_ALL_SLICES_FOR_PROJECTION) {
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startSllice = 1;
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endSlice = SLICE_COUNT;
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}
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run("Z Project...", "start=" + startSlice + " stop=" + endSlice +" projection=" + "[" + PROJECTION_METHOD + "]");
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selectImage(currentTitle);
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close();
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rename(currentTitle);
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}
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macro 'Lif2Tif Action Tool Options' {
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showOptionsDialog()
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}
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macro 'Lsm2Tif Action Tool Options' {
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showOptionsDialog()
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}
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macro 'Zvi2Tif Action Tool Options' {
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showOptionsDialog()
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}
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function showOptionsDialog() {
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Dialog.create("Tif Export Options");
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Dialog.addMessage("Projection Options");
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Dialog.addCheckbox("do z-projection", DO_PROJECTION);
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Dialog.addCheckbox("use all slices for projection", USE_ALL_SLICES_FOR_PROJECTION);
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Dialog.addNumber("start slice for projection", PROJECTION_START_SLICE);
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Dialog.addNumber("end slice for projection", PROJECTION_END_SLICE);
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Dialog.addChoice("projection method", newArray("Average Intensity", "Max Intensity", "Min Intensity", "Sum Slices", "Standard Deviation", "Median"), PROJECTION_METHOD);
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Dialog.addMessage("Colour Options");
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Dialog.addString("Channels for RGB-overlay (1-use, 0-skip):", CHANNELS_STRING);
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Dialog.show();
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DO_PROJECTION = Dialog.getCheckbox();
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USE_ALL_SLICES_FOR_PROJECTION = Dialog.getCheckbox();
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PROJECTION_START_SLICE = Dialog.getNumber();
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PROJECTION_END_SLICE = Dialog.getNumber();
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PROJECTION_METHOD = Dialog.getChoice();
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CHANNELS_STRING = Dialog.getString();
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}
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