Fiji<\/strong><\/a> is an image processing package \u2014 a “batteries-included” distribution of ImageJ, bundling many plugins which facilitate scientific image analysis. <\/p>\n Fiji<\/strong> is mainly used through a java based interactive graphical user interface (GUI). On the CSF3 the GUI can be started remotely on a compute node as an interactive job<\/a>.<\/p>\n Fiji<\/strong> also provides a headless mode<\/strong>, which is suitable for running batch jobs in the CSF3. For more info on headless mode please read the official project documentation<\/a>.<\/p>\n Fiji is free software, licensed under the GNU General Public License. It builds on top of the ImageJ2 core, which is licensed under the permissive BSD 2-clause license. Plugins and other components have their own licenses<\/a>. <\/p>\n All CSF users may use this software, as long as they follow the license terms.<\/p>\n Before running fiji, load the module below:<\/p>\n To be able to run workflows that can utilise multiple CPU cores, in this case 8 cores:<\/p>\n Then after you have connected to a node:<\/p>\n Note the &<\/strong> at the end of the command. It instructs the shell to open the window and then return control to the terminal, in case you want to execute any other commands in the commandline. <\/p>\n Create a jobscript similar to the one below:<\/p>\n Then submit your jobscript from within the scratch directory: Overview Fiji is an image processing package \u2014 a “batteries-included” distribution of ImageJ, bundling many plugins which facilitate scientific image analysis. Fiji is mainly used through a java based interactive graphical user interface (GUI). On the CSF3 the GUI can be started remotely on a compute node as an interactive job. Fiji also provides a headless mode, which is suitable for running batch jobs in the CSF3. For more info on headless mode please read.. Read more »<\/a><\/p>\n","protected":false},"author":24,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-11564","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/11564","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/24"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=11564"}],"version-history":[{"count":11,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/11564\/revisions"}],"predecessor-version":[{"id":11704,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/11564\/revisions\/11704"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=11564"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
Set up procedure<\/h2>\n
\r\nmodule load apps\/binapps\/fiji\/2.16.0\r\n<\/pre>\n
Running the application<\/h2>\n
Running the GUI interactively from a compute node<\/h3>\n
\r\n# request an interactive session using 8 CPU cores for 1 hour \r\n[username<\/em>@login1[csf3] ~]$ srun-x11 -p interactive -n 1 -c 8 -t 0-1\r\n<\/pre>\n
\r\n[username<\/em>@node1201[csf3] ~]$ module load apps\/binapps\/fiji\/2.16.0\r\n[username<\/em>@node1201[csf3] ~]$ fiji &\r\n<\/pre>\n
Running a batch job in headless mode<\/h3>\n
\r\n#!\/bin\/bash --login\r\n#SBATCH -p multicore # Partition is required. Runs on an AMD Genoa hardware.\r\n#SBATCH -n 8 # (or --ntasks=) where numcores is between 2 and 168.\r\n#SBATCH -t 1-0 # Wallclock limit (days-hours). Required!\r\n # Max permitted is 7 days (7-0).\r\n\r\n# Load any required modulefiles. A purge is used to start with a clean environment.\r\nmodule purge\r\nmodule load apps\/binapps\/fiji\/2.16.0\r\n\r\nfiji --headless -macro path-to-Macro.ijm\r\n<\/pre>\n
\nsbatch jobscript<\/em><\/code><\/p>\nFurther info<\/h2>\n","protected":false},"excerpt":{"rendered":"