Run macros from the command line ImageJ command line options: -macro path [arg] -batch path [arg] -eval "macro code" Examples: cd /users/wayne/ImageJ/Conference/images imagej FluorescentCells.jpg imagej -eval "makeOval(90,90,300,300); fill;" imagej -eval "return getDirectory('current')" imagej -macro Polygon imagej -batch BatchMeasure.ijm /Users/wayne/ImageJ/Conference/images/ To create 'imagej' command: Unix: alias imagej 'java -Xmx400m -jar /Users/wayne/ImageJ/ij.jar -ijpath /Users/wayne/ImageJ' Windows: Add ImageJ folder to PATH environment variable