Java

The best way to start writing an ImageJ2 plugin (ImageJ2 developers call it command and not plugin) is to download the example command from github and modify it. There is a video tutorial on the whole workflow on how to do this on youtube.

AutoPilot is the open source project that hosts the general algorithm for fast and robust assessment of local image quality, an automated computational method for image-based mapping of the three-dimensional light-sheet geometry inside a fluorescently labeled biological specimen, and a general algorithm for data-driven optimization of the system state of light-sheet microscopes capable of multi-color imaging with multiple illumination and detection arms.

This plugin detects a minimum cost z-surface in a 3D volume. A z surface is a topographic map indicating the altitude z as a function of the position (x,y) in the image. The cost of the surface depends on pixel intensity the surface is going through. This plugin find the z-surface with the lowest intensity in an image.

The interactive Watershed Fiji plugin provides an interactive way to explore local maxima and threshold values while a resulting label map is updated on the fly.

After the user has found a reliable parameter configuration, it is possible to apply the same parameters to other images in a headless mode, for example via ImageJ macro scripting.

Biocat is a java based software that allows to perform image classification or segmentation using machine learning. Several algorithm for the classification are available.