Examples of available plugins

In this section, I will discuss a few plugins that are available for ImageJ, most of which have also been published in scientific journals. They will show you how to use ImageJ for advanced image processing, with different degrees of automation and user interaction. They also provide a few examples of the design of a plugin, either with its own interface or just as a single command that executes. Some of these examples also have their source code available so that you can see how the developers implemented their algorithms. Be aware that having the source code and being able to understand it fully might be difficult: depending on the level of documentation or comments in the code. It might be very difficult to completely retrace the functioning of the code. As a program grows and new functions and algorithms are added, it deviates more from a single core algorithm to a more convoluted group of files. Developers using the Javadoc capabilities available in IDEs...