title: Background fluorescence estimation and vesicle segmentation in live cell imaging with conditional random fields.
abstract: Image analysis applied to fluorescence live cell microscopy has become a key tool in molecular biology since it enables to characterize biological processes in space and time at the subcellular level. In fluorescence microscopy imaging, the moving tagged structures of interest, such as vesicles, appear as bright spots over a static or nonstatic background. In this paper, we consider the problem of vesicle segmentation and time-varying background estimation at the cellular scale. The main idea is to formulate the joint segmentation-estimation problem in the general conditional random field framework. Furthermore, segmentation of vesicles and background estimation are alternatively performed by energy minimization using a min cut-max flow algorithm. The proposed approach relies on a detection measure computed from intensity contrasts between neighboring blocks in fluorescence microscopy images. This approach permits analysis of either 2D + time or 3D + time data. We demonstrate the performance of the so-called C-CRAFT through an experimental comparison with the state-of-the-art methods in fluorescence video-microscopy. We also use this method to characterize the spatial and temporal distribution of Rab6 transport carriers at the cell periphery for two different specific adhesion geometries.
authors.forename: Thierry
authors.initials: T
authors.lastname: Pécot
authors.forename: Patrick
authors.initials: P
authors.lastname: Bouthemy
authors.forename: Jérôme
authors.initials: J
authors.lastname: Boulanger
authors.forename: Anatole
authors.initials: A
authors.lastname: Chessel
authors.forename: Sabine
authors.initials: S
authors.lastname: Bardin
authors.forename: Jean
authors.initials: J
authors.lastname: Salamero
authors.forename: Charles
authors.initials: C
authors.lastname: Kervrann
mesh_terms: D000465:Algorithms; D003584:Cytological Techniques / Q000379:methods*; D049452:Green Fluorescent Proteins; D006367:HeLa Cells; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D049408:Luminescent Agents; D008856:Microscopy, Fluorescence / Q000379:methods*; D018715:Microscopy, Video; D020691:rab GTP-Binding Proteins
chemical_list: D049408:Luminescent Agents; C094135:Rab6 protein; D049452:Green Fluorescent Proteins; D020691:rab GTP-Binding Proteins