title: A detailed analysis of 3D subcellular signal localization.
abstract: Detection and localization of fluorescent signals in relation to other subcellular structures is an important task in various biological studies. Many methods for analysis of fluorescence microscopy image data are limited to 2D. As cells are in fact 3D structures, there is a growing need for robust methods for analysis of 3D data. This article presents an approach for detecting point-like fluorescent signals and analyzing their subnuclear position. Cell nuclei are delineated using marker-controlled (seeded) 3D watershed segmentation. User-defined object and background seeds are given as input, and gradient information defines merging and splitting criteria. Point-like signals are detected using a modified stable wave detector and localized in relation to the nuclear membrane using distance shells. The method was applied to a set of biological data studying the localization of Smad2-Smad4 protein complexes in relation to the nuclear membrane. Smad complexes appear as early as 1 min after stimulation while the highest signal concentration is observed 45 min after stimulation, followed by a concentration decrease. The robust 3D signal detection and concentration measures obtained using the proposed method agree with previous observations while also revealing new information regarding the complex formation.
authors.affiliation: The Centre for Image Analysis, Uppsala University, Uppsala, Sweden. amalka@cb.uu.se
authors.forename: Amalka
authors.initials: A
authors.lastname: Pinidiyaarachchi
authors.forename: Agata
authors.initials: A
authors.lastname: Zieba
authors.forename: Amin
authors.initials: A
authors.lastname: Allalou
authors.forename: Katerina
authors.initials: K
authors.lastname: Pardali
authors.forename: Carolina
authors.initials: C
authors.lastname: Wählby
mesh_terms: D000465:Algorithms; D000818:Animals; D002451:Cell Compartmentation / Q000502:physiology; D002478:Cells, Cultured; D019044:Image Cytometry / Q000295:instrumentation / Q000379:methods*; D046911:Macromolecular Substances / Q000032:analysis; D051379:Mice; D008856:Microscopy, Fluorescence / Q000295:instrumentation / Q000379:methods*; D009685:Nuclear Envelope / Q000502:physiology / Q000648:ultrastructure*; D012815:Signal Processing, Computer-Assisted; D051899:Smad2 Protein / Q000032:analysis; D051901:Smad4 Protein / Q000032:analysis; D012984:Software / Q000639:trends*
chemical_list: D046911:Macromolecular Substances; D051899:Smad2 Protein; C497783:Smad2 protein, mouse; D051901:Smad4 Protein; C490810:Smad4 protein, mouse