I am new to the Java ecosystem and build tools, so I am still not sure how the different maven repositories and what not work. Kyle Harrington, Curtis Rueden, and Kevin W. I will add just the basic ImageJ ones at this point, along with a really cool project called FunImageJ, which provides a Lisp (Clojure) interface for image analysis in ImageJ. Now there are a lot of dependencies I may need to work with ImageJ, including SciJava, ImageLib2, and many others. ![]() This gives the following directory structure: I'd recommend using Fiji if you are following along. I'll refer to ImageJ and Fiji interchangeably in this document, but note that I am using Fiji Version 2.0.0-rc-69/1.52i on Mac OSX. In this work in progress I will document how I set up my environment and any issues I had while developing and compiling a plugin. I want to develop ImageJ plugins using Clojure, and compile them to native Java bytecode. ImageJ plugins allow users to extend ImageJ functionality and ImageJ provides the means to easily share those changes with others. One of the best parts of this software is the extensibility. This powerful and vibrant ecosystem is build around the Java Virtual Machine (JVM) to allow for fast, cross-platform scientific image analysis. ![]() "Fiji: an open-source platform for biological-image analysis"."ImageJ2: ImageJ for the next generation of scientific image data".Here are some papers about the ImageJ ecosystem: ImageJ and Fiji (a batteries included ImageJ distribution) are amazing pieces of free software originally developed at the National Institutes of Health by Wayne Rasband (who still maintains the original ImageJ software), with newer versions currently developed by Curtis Reuden et al.
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