Drag and drop the desired folder into the Commander list.To extract the paths of all TIFF images in a directory:.To access Commander’s built-in help: type !HELP and press ↵ Enter.To reveal the directory of active image: type !IMP and press ↵ Enter, then choose Reveal Path.To access all JavaScript lib files: type !LIB and press ↵ Enter, then.To access ImageJ’s LUT folder: type !LUT and press ↵ Enter.Some of these ( cd, ls, pwd, etc.) are reminiscent of commands found in most command-line interfaces. Features include: drag-and-drop support, interaction with native file manager, regex filtering, and a built-in console for common operations.Ĭonsole mode is triggered by typing !, which evokes a list of searchable commands so that all file navigation can be done exclusively with the keyboard. It serves two purposes: 1) to expedite the opening of files and 2) to produce filtered lists of directory contents. It is a productivity tool that applies the principles of the search bar to file browsing, providing instant access to files just by typing abbreviations of filenames. Since the majority of BARs are scripts stored in dedicated files, BAR features Commander ( BAR › BAR Commander…), a keyboard-based file browser that produces filtered lists of directory contents. To have BARs immediately available when such toolsets are loaded, just append the same run("Move Menu (ContextMain)") call described above for StartupMacros. Any toolset loaded via the “>” More Tools drop down menu can define its own contextual menu (as detailed in the ImageJ User Guide, the contextual menu is controlled by a macro called Popup Menu that gets loaded at startup).This is intentional because all ImageJ commands must have unique names. The several Move Menu (ContextMain) commands across BAR submenus do not use the same label and are distinguishable by extra trailing spaces.For a slow setup requiring at least 1 second (1000 milliseconds), the pasted code would look something like this: This can be achieved through the built-in macro function wait(). It may be wise to allow ImageJ enough time to register all scripts before triggering transfers to the context menu. Open the Edit › Options › Startup… window and paste the string generated by the Macro Recorder into its text area so that ImageJ can run the command at every startup.Run BAR › Segmentation › Move Menu (ContextMain).Start the Macro Recorder ( Plugins › Macros › Record…).So, e.g., to install BAR › Segmentation in the context menu, one would: However, it is macro recordable which means it can be imposed at startup, using the ImageJ macro language. The shuttling mechanism is not permanent, i.e., it will not be remembered across restarts. The transfer is bidirectional: once in the context menu, running the same command will place the submenu back in the main menu bar. Context MenuīAR features a neat mechanism that allows BAR commands to shuttle between the main menu bar and the image's context menu.īAR submenus can be appended to the image’s context menu (the menu that pops up when right-clicking on the image canvas) by running BAR › › Move Menu (ContextMain). For pre-compiled java plugins, the source code is available through the About BAR… command. You can open any BAR script by holding ⇧ Shift while selecting its name from the BAR menu. Tools and ToolsetsĪs with all ImageJ commands, BAR scripts can be accessed in multiple ways: 1) through the BAR menu, 2) the Context Menu, 3) Keyboard Shortcuts, 3) the Shortcuts Menu Tool ( BAR › Tool Installers › Install Shortcuts Menu), that registers frequently used commands in the ImageJ toolbar, 4) by pressing L, or 5) from other scripts, macros and plugins. Wipe Background Snippets, BAR lib and Tutorialsĭescribed in Scripting BARs. List of BARsĭistribution Plotter, Find Peaks, Fit Polynomial, Interactive Plotting Segmentation Remember: You can open all the scripts using the ⇧ Shift key. Nevertheless, all files contain useful commentary at the top of the source code file. Some of the scripts have a dedicated documentation page, others feature built-in help, while a handful were deemed too simple to require dedicated instructions. All routines should be documented on GitHub. Enjoy BAR! DescriptionīAR files are accessible through a dedicated top-level menu subdivided in task-oriented categories. Activate the BAR checkbox in the alphabetically-sorted list of update sites. Run Help › Update… and choose Manage update sites. It is curated using GitHub and distributed as an optional update site. The collection contains Macros, Scripts and Plugins focused on Data Analysis, Image Annotation and Image Segmentation. If you’d like to help, check out the how to help guide!īAR: A collection of Broadly Applicable Routines. The content of this page has not been vetted since shifting away from MediaWiki.
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