Sorry I didn’t get around to answering this sooner. The problem is that you’re executing an ImageJ 1.0 macro in RunImageJ.
Caused by: java.awt.HeadlessException
ImageJ 1.0 isn’t headless, so we have to start up the ImageJ UI to run the macro - perhaps there is some work-around that we could do to run the macro headless and hope that no AWT calls are made. The error occurs when we start the UI and AWT rejects our request because Java is headless. ImageJ 2.0 is designed to ensure that headless operations work, so for scripts other than macros and ImageJ 2.0 plugins, you can truly run headless.
There’s a trick we use here on our cluster to run ImageJ 1.0 macros. If you define the environment variable, “CELLPROFILER_USE_XVFB”, then CellProfiler itself will run in headless-style on the command-line, but it will start Java in non-headless mode so that UI can be done. On our Linux cluster, we use XVFB (http://en.wikipedia.org/wiki/Xvfb) to mimic the display. On Windows, you’ll get a lot of annoying windows popping up, but other than that, it should operate as if it were headless.
Let me know if defining CELLPROFILER_USE_XVFB works for you. If not, maybe we can put in something to disable ImageJ 1.0 UI display and we can see if the macros execute correctly.