The download section contains scripts written in the Jython and BeanShell languages. Step-by-step instructions in this tutorial are provided for developing scripts in Jython.
BeanShell: Syntax similar to Java, versatileįiji provides a richer programming environment than ImageJ and it is recommended to use Fiji instead of ImageJ for any script development. 
Jython: Python syntax with a few limitations, easy to learn, very versatile. ImageJ macro language: simple, slow, not very versatile. The API is well documented on these public sites:įiji provides convenient programming wrappers for these Java classes so you can write your scripts in: The application programming interface (API) defines the various Java packages, classes, methods, and constants that a programmer can use for development of custom Fiji & ImageJ scripts. The Application Programming Interface (API)įiji and ImageJ are written in Java. This tutorials landing page and click on the Code button. Linux: The Fiji application should be installed in a directory where the user has read, execution, and write permissions, e.g. Windows 7 & 10: The Fiji application should be installed in the the user’s home directory rather than the default C:\Program Files directory. MacOS X: The Fiji application should be installed in the the user’s home directory rather than the default Applications folder. It is available for Mac OSX, Windows, and Linux platforms. 
Intro & Fiji Programming Tools Installationįiji is a stand-alone application that can be downloaded from theįiji website. Example scripts are provided for the Jython and BeanShell languages. Step-by-step instructions are provided for developing scripts in Jython, an implementation of the popular Python language for Java platforms.
Fiji vs imagej how to#
Here you will learn how to write scripts for automated execution of image processing pipelines and batch processing of multiple image files in Fiji.
This tutorial 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.
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