toggle imagej2 options at command line

I am using Fiji at the command line in headless mode and running commands using a macro. I am working in a server environment using Ubuntu 14.04 (trusty). The images I am trying to work on our saved in the OME.TIFF format and I am trying to using the "open(path)" macro command with ImageJ2 options enabled.

When I download Fiji in the server it seems as if ImageJ2 options are not enabled by default (I get an error telling me there are no images open). Since I do not have a desktop environment, I use a local machine with the same version of Ubuntu to start Fiji and enable the ImageJ2 options. I then tar and move this version of Fiji to the server. However, when I try to run my macro I get the same "no images open" error message which seems to suggest that the ImageJ2 options are again disabled.

It would be great to toggle the ImageJ2 options at the command line (or indeed from a macro) so that macros can take advantage of SCIFIO when running headless in a server environment.

Cheers,

Dan.

Start by tracing the headless command-line launch and the macro open(path) entry point, then determine where ImageJ2 options are enabled. Check how SCIFIO handles OME.TIFF input in this mode. Done means a command-line or macro toggle reliably enables ImageJ2 options and allows the documented headless workflow to open the image.

Written by the indexing model from the issue text.