Robust methods for segmentation and tracking are critical for quantitative biology. We give an overview of our recent work on graph based methods for various microscopy image analysis, including tracing over 3-D electron microscopy image stacks, tracking in time-lapse confocal image sequences, and 3D segmentation. We present results on a variety of datasets such as 3-D confocal membrane volumes of the ascidian Ciona, electron micrograph stacks from the rabbit retina, and bright field microscopy time sequence data from mouse retina.