{"id":652,"date":"2016-06-29T10:48:32","date_gmt":"2016-06-29T10:48:32","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/icsf\/?page_id=652"},"modified":"2019-11-27T16:10:10","modified_gmt":"2019-11-27T16:10:10","slug":"imagejfiji","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/imagejfiji\/","title":{"rendered":"ImageJ and Fiji"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/imagej.nih.gov\/ij\/\">ImageJ<\/a> is a program to display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images.<\/p>\n<p><a href=\"http:\/\/fiji.sc\/\">Fiji<\/a> is an enhanced version of <a href=\"http:\/\/imagej.net\/ImageJ2\">ImageJ2<\/a> (which itself is an enhancement of ImageJ supporting multi-dimensional data) containing many more 3rd party plugins that extend the functionality of ImageJ.<\/p>\n<p>Version 1.51i of ImageJ and versions 2.0.0, 2.1.2 (based on ImageJ 1.51d, 1.52p) of Fiji are installed on the iCSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing ImageJ and Fiji on the iCSF. However users are requested to cite the applications in any publications. Please see the <a href=\"http:\/\/imagej.net\/Citing\">ImageJ citation instructions<\/a> for further details.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load <em>one<\/em> of the following modulefiles:<\/p>\n<pre>\r\n# Fiji - enhanced ImageJ\r\nmodule load apps\/binapps\/fiji\/2.1.2        # Provides ImageJ 1.52p\r\nmodule load apps\/binapps\/fiji\/2.0.0        # Provides ImageJ 1.51d\r\n\r\n# Or original ImageJ\r\nmodule load apps\/binapps\/imagej\/1.51i\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Depending which modulefile has been loaded (see above) you can then run the following command at the iCSF command-line:<\/p>\n<pre>\r\nImageJ\r\n\r\n# or\r\n\r\nfiji\r\n<\/pre>\n<p>If the Fiji modulefile has been loaded you will get a warning message saying:<\/p>\n<pre>\r\n[WARNING] Your ImageJ installation cannot be updated because it is read-only\r\n<\/pre>\n<p>This can safely be ignored.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/imagej.nih.gov\/ij\/\">ImageJ website<\/a><\/li>\n<li><a href=\"http:\/\/fiji.sc\/\">Fiji website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview ImageJ is a program to display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. Fiji is an enhanced version of ImageJ2 (which itself is an enhancement of ImageJ supporting multi-dimensional data) containing many more 3rd party plugins that extend the functionality of ImageJ. Version 1.51i of ImageJ and versions 2.0.0, 2.1.2 (based on ImageJ 1.51d, 1.52p) of Fiji are installed on the iCSF. Restrictions on use There are no restrictions on.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/imagejfiji\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":43,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-652","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/652","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/comments?post=652"}],"version-history":[{"count":8,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/652\/revisions"}],"predecessor-version":[{"id":1028,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/652\/revisions\/1028"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/43"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/media?parent=652"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}