ImageJ Macro to 3D project all images in directory

3d-project-all.ijm

// ImageJ Macro to 3D project all images in directory
//
// Created by Thomas Miedema
// February 15th 2014
//
// Tested with:         ImageJ  = 1.48q
// Probably works with: ImageJ >= 1.47o
// Doesn't work with:   ImageJ  = 1.46a

// rsb.info.nih.gov/ij/developer/macro/functions.html

// Do not display images.
setBatchMode(true)

inputDirectory = getDirectory("");
outputDirectory = getDirectory("");

list = getFileList(inputDirectory);
for (i = 0; i < list.length; i++) {
    open(inputDirectory + list[i]);

    run("Set Scale...", "distance=1 known=0.166 pixel=1 unit=um global");
    setSlice(nSlices / 2);
    resetMinAndMax();
    run("3D Project...", "projection=[Brightest Point] axis=Y-Axis slice=0.3 initial=0 total=360 rotation=10 lower=1 upper=255 opacity=0 surface=100 interior=50 interpolate");

    saveAs("Tiff", outputDirectory + File.nameWithoutExtension + "-3dprojection");
    close();
    close();
}

setBatchMode(false)