Batch conversion to pyramidal ome-tiff using Glencoe Software optimized workflow #BIOP #Fiji #OmeTiff #MRXS

bf2ometiff.groovy

/* Batch conversion of files to OME-TIFF following this install:
 * https://c4science.ch/w/bioimaging_and_optics_platform_biop/image-processing/qupath/ome-tiff-conversion/
 *  
 * Uses bioformats2raw and raw2ometiff
 * https://www.glencoesoftware.com/blog/2019/12/09/converting-whole-slide-images-to-OME-TIFF.html
 *  
 * Works with MRXS files
 *
 * Nicolas BIOP, EPFL, 2021
 */
 
 
#@File(label = "File to convert to ome.tiff") originalFile
#@Integer(label = "Number of resolution levels", value = 5) nResolutions
#@Boolean(label = "Check if this is a RGB image") isRGB
#@String(label = "Compression", choices = {"Uncompressed", "LZW", "JPEG-2000", "JPEG-2000 Lossy","JPEG", "zlib"}, value = "LZW") compression
 
bf2rawPath = "bioformats2raw.bat"
raw2ometiffPath = "raw2ometiff.bat"

// First step : create a temporary dir for raw data
String tmpdir = Files.createTempDirectory("raw2ometiff").toFile().getAbsolutePath();

// Starts the command
List<String> cmd = new ArrayList<>();

// bioformats2raw.bat --resolutions=4 source dest
cmd.add(bf2rawPath)
cmd.add("--resolutions="+nResolutions)
cmd.add(originalFile.getAbsolutePath())
cmd.add(tmpdir+File.separator+"raw")

println("Tmp folder = "+tmpdir+File.separator+"raw")

ProcessBuilder pb = new ProcessBuilder(cmd);
println("- Starting conversion to raw data (1/2) "+originalFile.getAbsolutePath())
Process p = pb.inheritIO().start();
p.waitFor();
println("- Done")

// raw2ometiff.bat --compression="LZW" source dest.tiff

def ometiffFileName = FilenameUtils.removeExtension(originalFile.getAbsolutePath())+".ome.tiff"; 

cmd.clear()
cmd.add(raw2ometiffPath)
cmd.add("--compression="+compression)
cmd.add("--progress")
cmd.add(tmpdir+File.separator+"raw")
cmd.add(ometiffFileName)

pb = new ProcessBuilder(cmd);
//pb.redirectInput(ProcessBuilder.Redirect.INHERIT);
//pb.redirectOutput(ProcessBuilder.Redirect.INHERIT);

println("- Starting writing as ome.tiff (2/2) : "+ometiffFileName)
p = pb.inheritIO().start();
p.waitFor();
println("- Done")

println("Cleaning raw temp data");
FileUtils.deleteDirectory(new File(tmpdir+File.separator+"raw"));
println("- Done");

import java.io.*
import java.util.ArrayList
import java.util.List
import java.nio.file.Files
import org.apache.commons.io.FilenameUtils
import org.apache.commons.io.FileUtils

import ij.IJ
import ij.Prefs