title: Topographic prominence as a method for cluster identification in single-molecule localisation data.
abstract: Single-molecule localisation based super-resolution fluorescence imaging produces maps of the coordinates of fluorescent molecules in a region of interest. Cluster analysis algorithms provide information concerning the clustering characteristics of these molecules, often through the generation of cluster heat maps based on local molecular density. The goal of this study was to generate a new cluster analysis method based on a topographic approach. In particular, a topographic map of the level of clustering across a region is generated based on Getis' variant of Ripley's K-function. By using the relative heights (topographic prominence, TP) of the peaks in the map, cluster characteristics can be identified more accurately than by using previously demonstrated height thresholds. Analogous to geological TP, the concepts of wet and dry TP and topographic isolation are introduced to generate binary maps. The algorithm is validated using simulated and experimental data and found to significantly outperform previous cluster identification methods. Illustration of the topographic prominence based cluster analysis algorithm.
authors: Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, Hodgkin Building, Guy's Campus, London, SE1 1UL, United Kingdom.
authors: Juliette
authors: J
authors: Griffié
authors: Section of Immunology, Division of Infectious Diseases, Faculty of Medicine, Imperial College London, Praed Street, St Mary's Campus, London, United Kingdom.
authors: Lies
authors: L
authors: Boelen
authors: Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, Hodgkin Building, Guy's Campus, London, SE1 1UL, United Kingdom.
authors: Garth
authors: G
authors: Burn
authors: Academic Department of Rheumatology, Division of Immunology, Infection and Inflammatory Disease, Faculty of Life Sciences and Medicine, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, United Kingdom.
authors: Andrew P
authors: AP
authors: Cope
authors: Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, Hodgkin Building, Guy's Campus, London, SE1 1UL, United Kingdom. dylan.owen@kcl.ac.uk.
authors: Dylan M
authors: DM
authors: Owen
mesh_terms: D000465:Algorithms; D018929:Cell Culture Techniques; D002465:Cell Movement; D016000:Cluster Analysis; D003198:Computer Simulation; D006801:Humans; D018799:Intercellular Adhesion Molecule-1 / Q000378:metabolism; D016169:Lymphocyte Function-Associated Antigen-1 / Q000378:metabolism; D008856:Microscopy, Fluorescence / Q000379:methods*; D057054:Molecular Imaging / Q000379:methods*; D013601:T-Lymphocytes / Q000166:cytology / Q000502:physiology
chemical_list: C573420:ICAM1 protein, human; D016169:Lymphocyte Function-Associated Antigen-1; D018799:Intercellular Adhesion Molecule-1
keywords: T-lymphocytes; cluster analysis; lymphocyte function-associated antigen-1; microscopy