[Convert Images to Pyramids using QuPath in Parallel] this is pretty fast and works for RGB images. To run in Fiji #fiji #qupath #ome-tiff

Convert Images Using QuPath.groovy

#@ File imagesDirectory (label="Directory with images", style="directory")
#@ String extension (label="Image extension", value="tif")
#@ String quPathExe (label="Path to QuPath Executable", value="C:/QuPath-0.3.2/QuPath-0.3.2 (console).exe")

import groovyx.gpars.GParsPool

def folder = imagesDirectory

def convertedFolder = new File( folder.getParent(), "converted")
convertedFolder.mkdirs()

def fileList = folder.listFiles().findAll{ it.getName().endsWith(extension) && !it.getName().contains("Overview") }


GParsPool.withPool(6) {
	fileList.eachParallel{ file ->
		println file
		
		def cmd = quPathExe
		def outputFile = new File (folder, file.getName() + "_info.txt")
		
		def pb = new ProcessBuilder(cmd, "convert-ome", file.getAbsolutePath(), new File( convertedFolder, file.getName()+".ome.tiff").getAbsolutePath(), "-p", "-t", "1")
						.redirectErrorStream(true)
						.redirectOutput(outputFile)
		
		println pb.command()
		pb.start().waitFor()
	}
}

//"QuPath-0.3.2 (console).exe" convert-ome Y:\temp-Oli\weird_tif\15936.tif Y:\temp-Oli\weird_tif\15936.ome.tiff -p -t 1