title: Geometric approach to segmentation and protein localization in cell culture assays.
abstract: Cell-based fluorescence imaging assays are heterogeneous and require the collection of a large number of images for detailed quantitative analysis. Complexities arise as a result of variation in spatial nonuniformity, shape, overlapping compartments and scale (size). A new technique and methodology has been developed and tested for delineating subcellular morphology and partitioning overlapping compartments at multiple scales. This system is packaged as an integrated software platform for quantifying images that are obtained through fluorescence microscopy. Proposed methods are model based, leveraging geometric shape properties of subcellular compartments and corresponding protein localization. From the morphological perspective, convexity constraint is imposed to delineate and partition nuclear compartments. From the protein localization perspective, radial symmetry is imposed to localize punctate protein events at submicron resolution. Convexity constraint is imposed against boundary information, which are extracted through a combination of zero-crossing and gradient operator. If the convexity constraint fails for the boundary then positive curvature maxima are localized along the contour and the entire blob is partitioned into disjointed convex objects representing individual nuclear compartment, by enforcing geometric constraints. Nuclear compartments provide the context for protein localization, which may be diffuse or punctate. Punctate signal are localized through iterative voting and radial symmetries for improved reliability and robustness. The technique has been tested against 196 images that were generated to study centrosome abnormalities. Corresponding computed representations are compared against manual counts for validation.
authors.affiliation: Lawerence Berkeley National Laboratory, 1 Cyclotron Road, Berkley, CA 94720, USA. sraman@lbl.gov
authors.forename: S
authors.initials: S
authors.lastname: Raman
authors.forename: C A
authors.initials: CA
authors.lastname: Maxwell
authors.forename: M H
authors.initials: MH
authors.lastname: Barcellos-Hoff
authors.forename: B
authors.initials: B
authors.lastname: Parvin
mesh_terms: D000465:Algorithms; D018929:Cell Culture Techniques; D002460:Cell Line; D005260:Female; D006801:Humans; D007091:Image Processing, Computer-Assisted; D008856:Microscopy, Fluorescence / Q000379:methods / Q000706:statistics & numerical data; D008954:Models, Biological; D011506:Proteins / Q000378:metabolism*; D012984:Software; D013347:Subcellular Fractions / Q000378:metabolism*
chemical_list: D011506:Proteins