ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection.
Trainable Weka Segmentation: A Fiji plugin that combines a collection of machine learning algorithms with a set of selected image features to produce pixel-based segmentations using Weka. Provides a framework to use and compare any available classifier to perform image segmentation based on pixel classification, bridging machine learning and image processing. Has GUI support.
CDeep3M: Plug-and-Play cloud based deep learning for image segmentation of light, electron and X-ray microscopy