/** * Colony Count Macro * Collaborators: Guillaume MARTIN, ISEM UMR 5554, UM2 * Automatically count E. Coli colonies in petri dishes. The software uses the * Macro_IO_Settings plugin (http://www.mri.cnrs.fr/index.php?m=82) * from the Remote ImageJ project. * The image analysis uses a grayscale watershed algorithm. Note that the control images * contain an overlay that shows the objects that have been found. Use * Image>Overlay>To Roi Manager to transform the overlay into rois. * * (c) 2010, INSERM * written by Volker Baecker at Montpellier RIO Imaging (www.mri.cnrs.fr) */ 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; } run("Table...", "name=Counts width=350 height=250"); print("[Counts]", "\\Headings:name\tcount"); run("ROI Manager..."); for (i=0; i