[ome-devel] HPC/OMERO integration

[Alex Herbert]

Hi Curtis, Johannes,

Thanks for the help with the ImageJ headless situation. I would like to 
try ImageJ2 if you think it will support BioFormats from within 
command-line macros.

I decided to go down the route of building my own headless.jar having 
read about the solution used in Fiji. I found some old code for the 
headless modifications but it was based on an old version of ImageJ and 
changes to ImageJ since meant that I could not run my plugin. I cannot 
even remember what did not work but having seen how easy it was to 
modify the code I just did it myself using the latest stable release of 
the relevant ImageJ classes. My headless system now works fine and I 
have complete source control of the changes so can fully support my 
environment.

I did not know about the new Javassist workaround. I will have to try 
running Fiji with my command-line macros and see if it works OK. This 
will mean that I wouldn't have to maintain my headless code.

My unsolved issue is not being able to use BioFormats. Thanks for adding 
some extra insight to this problem. Having looked at the code (and used 
the plugin) I know it modifies the GenericDialog. But I did not persist 
with my investigations as I now load my images using the native TIFF 
support in ImageJ (this was a path of least resistance). It would be 
nice to use BioFormats to read OME-TIFFs from OMERO and avoid having to 
do extra work with lots of single plane TIFFs.

I would be happy to try using ImageJ2 as the engine for my server 
scripts if it works with BioFormats support. However I have failed to 
find documentation on ImageJ2 and running it with some options like -h, 
-help, --help did not give any clues. If you could provide me with an 
example for the command-line mode I will try it out.

Regards,

Alex