A novel three-dimensional variant of the watershed transform for segmentation of electron density maps

• Published in: Journal of structural biology Vol. 138; no. 1; pp. 123 - 129
• Main Author: Volkmann, Niels
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-04-2002
• Subjects: Actin Cytoskeleton - chemistry; Actin Cytoskeleton - ultrastructure; Actomyosin - chemistry; Actomyosin - ultrastructure; Algorithms; Animals; Automated segmentation; Cellular Structures - ultrastructure; Electron cryomicroscopy; Electron tomography; Feature extraction; Foot-and-Mouth Disease Virus - ultrastructure; Golgi Apparatus - ultrastructure; Humans; Image processing; Imaging, Three-Dimensional - methods; Mathematical morphology; Microscopy, Electron - methods; Muscle Proteins - chemistry; Muscle Proteins - ultrastructure; Pattern recognition; Tomography, X-Ray Computed - methods; Image processing; Electron cryomicroscopy; Automated segmentation; Electron tomography; Feature extraction; Pattern recognition; Mathematical morphology
• ISSN: 1047-8477; 1095-8657
• DOI: 10.1016/S1047-8477(02)00009-6

Electron density maps at moderate resolution are often difficult to interpret due to the lack of recognizable features. This is especially true for electron tomograms that suffer in addition to the resolution limitation from low signal-to-noise ratios. Reliable segmentation of such maps into smaller, manageable units can greatly facilitate interpretation. Here, we present a segmentation approach targeting three-dimensional electron density maps derived by electron microscopy. The approach consists of a novel three-dimensional variant of the immersion-based watershed algorithm. We tested the algorithm on calculated data and applied it to a wide variety of electron density maps ranging from reconstructions of single macromolecules to tomograms of subcellular structures. The results indicate that the algorithm is reliable, efficient, accurate, and applicable to a wide variety of biological problems.