/** * MRI Artemia Tools * * The Artemia Tools help to calculate the normalized redness of Artemia in images * * written 2011-2013 by Volker Baecker (INSERM) at Montpellier RIO Imaging (www.mri.cnrs.fr) * in collaboration with Nicolas Rode and Eva Lievens * */ var helpURL = "http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Artemia_Tools" macro "Unused Tool - C037" { } macro "MRI Artemia Tools Action Tool - C762D3eD5bD68D69D6aD6eCcc9D29D3aD3bD56D8aD8bD95Dc3Dd2Cbb7D4aD4bD79D7aD87D88CcdaD1aD65D6fD9bDa3Db2Db4Cba4D59D5aD5cD67D6bD78CccaD74D96Cbc8D57D7cD84D89D97Dc2CcdbD7eD83D8dD93D9cDa6Caa5D4dD4eD5dD75D76D77D85Ccc9D2aD2bD38D8cD9aDa7Da8Da9Cbb8D3dD49D66D6dD86D98D99CcdbD19D1bD28D2cD37Da5Dd0De0De1Cbb7D4cD58D5eD6cD7bD94Db3CcdaD46D47D7dDaaDc1Ccc9D39D3cD48Da4Dd1" { run('URL...', 'url='+helpURL); } macro "01 artemia prepare Action Tool - C037T4d14p" { prepare(); } macro "02 artemia measure Action Tool - C037T4d14m" { measure(); } macro "03 artemia next image Action Tool - C037T4d14n" { nextImage(); } macro "04 artemia calculate redness Action Tool - C037T4d14c"{ calculateRedness(); } function prepare() { run("Conversions...", "scale"); run("Set Measurements...", "mean display redirect=None decimal=3"); run("RGB Stack"); setSlice(3); setAutoThreshold("Default dark"); setAutoThreshold("Default"); run("Threshold..."); } function measure() { // measure red composant in individuals resetThreshold(); roiManager("Deselect"); roiManager("XOR"); setSelectionName("xor") roiManager("Add"); roiManager("Select", 0); roiManager("Delete"); roiManager("Select", 0); roiManager("Delete"); run("Select None"); setSlice(1); roiManager("Measure"); setSlice(2); roiManager("Measure"); setSlice(3); roiManager("Measure"); roiManager("Delete"); } function nextImage() { // step 3 - next image setOption("Changes", false); run("Open Next"); } function calculateRedness() { // STEP 4 - calculate redness // ask for normalization area // calculate R/(R+G+B) waitForUser("Please select the normalization area"); setSelectionName("control"); roiManager("Add"); rednessValues = newArray(nResults / 3); labels = newArray(nResults / 3); for (i=0; i