scifio and headless fiji under linux

Posted by Daniel Matthews on Nov 10, 2014; 11:05pm
URL: http://imagej.273.s1.nabble.com/scifio-and-headless-fiji-under-linux-tp5010369.html

Hi

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.

Is there a way to enable ImageJ2 at the command line or in a config file?

Cheers,

Dan.