[ome-devel] HPC/OMERO integration

[Johannes Schindelin]

Hi,

On Thu, 1 Mar 2012, Curtis Rueden wrote:

> > I have used a similar approach to call ImageJ within OMERO scripts. I
> > had to overcome the Java headless problem (since my server does not
> > have an X environment and Java's AWT libraries on linux are tied to
> > the X server).  This was easy enough for ImageJ with a few custom
> > classes that do not show graphical objects. I can then call ImageJ
> > with a script to do any processing I like on the exported TIFFs.
>
> Fiji employs similar hacks. It used to have a special JAR file that was
> prepended to the classpath before ij.jar, but now we opt to use
> Javassist with runtime patching instead, as it is less susceptible to
> problems when ij.jar changes. You can launch scripts and plugins
> headlessly using the --headless option of the Fiji launcher. See:
>
> http://fiji.sc/wiki/index.php/Scripting_Help#Running_Scripts_in_Headless_Mode

See also http://fiji.sc/Headless

Ciao,
Johannes