In such a case I would like to log this event, stop the execution of that particular image and go on to the next. Is that somehow feasible? Even if I could just log the failure (together with the filename of the sequence) would be great.
One alternative I see for now is to not use sequence batch but run “single” protocols via a shell script from the command line and do a “throw(message)” in case something goes wrong.
Thanks already for any help or advice on this!
PS: The command line option seems not to work in my case as in the protocol I use the ImageJ plugin MorpholibJ and I receive in this mode the error: Unrecognized command: “Morphological Filters (3D)”. In GUI mode all runs fine.