A hack for calling the Bio-Formats Exporter programmatically.

ExporterWorkaround.java

import ij.IJ;
import ij.ImagePlus;
import ij.Macro;
import loci.plugins.LociExporter;

/**
 * This demonstrates how to programmatically call the Bio-Formats Exporter
 * plugin, working around ImageJ's limitation that macro-based executions must
 * be run in a thread named with a "Run$_" prefix. There is likely a simpler way
 * of doing it, but this solution works.
 */
public class ExporterWorkaround implements Runnable {

	private ImagePlus imp;

	public ExporterWorkaround(final ImagePlus imp) {
		this.imp = imp;
	}

	@Override
	public void run() {
		final LociExporter bfExporter = new LociExporter();
		final String file = "/Users/curtis/Desktop/clown.tif";
		final String macroOpts = "save=[" + file + "] compression=LZW";
		bfExporter.setup(null, imp);
		Macro.setOptions(macroOpts);
		bfExporter.run(null);
		IJ.showMessage("All done!");
	}

	public static void main(String... args) {
		// open a test image
		final ImagePlus imp =
			IJ.openImage("http://imagej.nih.gov/ij/images/clown.jpg");

		// launch the Bio-Formats Exporter in a special thread
		// NB: Must run in a thread with name starting with "Run$_"
		// https://github.com/fiji/ImageJA/blob/v1.47t/src/main/java/ij/Macro.java#L88
		final Thread t = new Thread(new ExporterWorkaround(imp), "Run$_Exporter");
		t.start();
		try {
			t.join();
		}
		catch (final InterruptedException e) {
			IJ.handleException(e);
		}
	}

}