Here you will learn how to write scripts for automated execution of image processing pipelines and batch processing of multiple image files in Fiji. See the Scripting Headless page for instructions on executing scripts headlessly.This chapter is an introduction to the scripting interface of theįiji application, an open-source and enhanced version of the popular ImageJ program used for scientific image processing. The original ImageJ recognizes plugins and scripts in. scripts/ as it is already described in the previous section, and for jars in. ImageJ2 (and therefore Fiji) looks for scripts in subfolders of. and therefore get added to the menu when the JAR is on the classpath (i.e. Inside the example-script-collection jar, the scripts are in. For this purpose, example-script-collection can be used as the template Maven project. Scripts can be packaged in a JAR file for easier distribution to your colleagues and via Update Sites. Use the macro recorder to get the required code for doing so. If you aren’t able to find your script, you can always use the search bar to verify its location (or absence).Ĭommands added to the menu in the described way can be called from other scripts. Scripts can be placed in other menus by nesting subdirectories, for example placing a script in the ImageJ2.app/scripts/File directory will add it to the File menu. Scripts in the top-level ImageJ2.app/plugins directory will appear at the bottom of the Plugins menu. The extension will be stripped and any underscores will be turned into spaces before the script is added to the menus. Adding scripts to the Plugins menuįor the script to appear in the menus, the following must apply:įiji users: replace ImageJ2.app with Fiji.app For details, please see the Script Editor documentation. You can create, edit and run scripts using the built-in Script Editor. Selecting and executing text from the screen ⇧ Shift + ↓ Down: move to the line below within the prompt.⇧ Shift + ↑ Up: move to the line above within the prompt.⇧ Shift + ↵ Enter: create a new line within the prompt.You can enlarge the prompt by dragging the middle bar. ↵ Enter: execute the contents of the prompt.↑ Up: bring the previously typed command.Using an interpreterĪll scripting languages use the same basic interpreter, with the following common features. See the script parameters page for details. This approach is preferred to using GenericDialog because it is totally agnostic to the user interface, allowing such scripts to run in a variety of contexts. There is a universal script parameter notation available across all scripts for declaring inputs and outputs. Scala support is currently experimental, and has bugs. It is nearly 100% compatible with Java syntax, but so is Groovy. See the MATLAB Scripting page for details.īeanShell is an old script language, maintained mostly for backwards compatibility. ImageJ2 can interface bidirectionally with MATLAB. This is the most difficult path, but also the most powerful. You can code Java plugins in the Script Editor. R is a popular choice among scientists and statisticians. Lisp is a popular choice among computer scientists. Ruby is another popular choice among web developers. JavaScript is a popular choice among web developers. You can write (/scripting/jython) (a Java-based Python 2 dialect) from inside ImageJ using its (/scripting/script-editor), or use (/scripting/pyimagej) to invoke ImageJ functions from Python scripts. Python is a popular choice among scientists. The ImageJ macro language is less powerful than the other scripting languages, but is designed to be easy to learn and use. Learn this, and using Java later (if needed) will become easier. Groovy is a flexible and powerful scripting language, Java-like but less verbose and dynamically typed. The following table summarizes the possibilities. ImageJ2’s Script Editor supports many different languages. See Scripting comparisons for a side-by-side comparison of scripting languages.Grab code snippets for common tasks from the Scripting toolbox.Otherwise, choose your language from the Language menu.Optionally, choose a template from the Templates menu to get you started.Press the [ key to open the Script Editor (or ⇧ Shift- [ to open the Script Interpreter).Read the ImageJ2 tutorial notebooks to learn how to write scripts.ImageJ2 allows you to write scripts in several different languages. If you’d like to help, check out the how to help guide! The content of this page has not been vetted since shifting away from MediaWiki.
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