title: Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography.
abstract: Electron tomography is a promising technology for imaging ultrastructures at nanoscale resolutions. However, image and quantitative analyses are often hindered by high levels of noise, staining heterogeneity, and material damage either as a result of the electron beam or sample preparation. We have developed and built a framework that allows for automatic segmentation and quantification of filamentous objects in 3D electron tomography. Our approach consists of three steps: (i) local enhancement of filaments by Hessian filtering; (ii) detection and completion (e.g., gap filling) of filamentous structures through tensor voting; and (iii) delineation of the filamentous networks. Our approach allows for quantification of filamentous networks in terms of their compositional and morphological features. We first validate our approach using a set of specifically designed synthetic data. We then apply our segmentation framework to tomograms of plant cell walls that have undergone different chemical treatments for polysaccharide extraction. The subsequent compositional and morphological analyses of the plant cell walls reveal their organizational characteristics and the effects of the different chemical protocols on specific polysaccharides.
authors.affiliation: Life Sciences Division, Lawrence Berkeley Nat Lab.
authors.forename: Leandro A
authors.initials: LA
authors.lastname: Loss
authors.affiliation: Dept of Computer Science, University of Nevada, Reno.
authors.forename: George
authors.initials: G
authors.lastname: Bebis
authors.affiliation: Life Sciences Division, Lawrence Berkeley Nat Lab.
authors.forename: Hang
authors.initials: H
authors.lastname: Chang
authors.affiliation: Energy Biosciences Institute, Univ of California, Berkeley.
authors.forename: Manfred
authors.initials: M
authors.lastname: Auer
authors.affiliation: Energy Biosciences Institute, Univ of California, Berkeley.
authors.forename: Purbasha
authors.initials: P
authors.lastname: Sarkar
authors.affiliation: Life Sciences Division, Lawrence Berkeley Nat Lab.
authors.forename: Bahram
authors.initials: B
authors.lastname: Parvin
keywords: 3d segmentation; electron tomography; plant cell wall; tensor voting