/** * Estimate the amount of arabidopsis seedlings * Collaborators: Prof. David Macherel, UMR Physiologie Moléculaire des Semences, ARES, * université Angers * Use color thresholding to detect the amount of seedlings per well. * Automatic measurement of the six wells present in one image. * The macro uses the Macro_IO_Settings plugin (http://www.mri.cnrs.fr/index.php?m=82) * from the Remote ImageJ project. * * (c) 2010, INSERM * written by Volker Baecker at Montpellier RIO Imaging (www.mri.cnrs.fr) */ // reset imagej settings run("Colors...", "foreground=white background=black selection=yellow"); run("Options...", "iterations=1 black count=1"); run("Set Measurements...", "area display redirect=None decimal=3"); run("Clear Results"); call("fr.cnrs.mri.macro.io.IOSettings.resetFileLists"); call("fr.cnrs.mri.macro.io.IOSettings.show"); waitForUser("Please select the input files using the IOSettings dialog and press ok"); setBatchMode(true); IJ.log("\\Clear"); list = call("fr.cnrs.mri.macro.io.IOSettings.getFileList"); files = split(list, ","); if (list=="none") { IJ.log("No files selected! Macro stopped."); return; } for (i=0; i