3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations

Motivation Single-molecule localization microscopy (SMLM) can play an important role in integrated structural biology approaches to identify, localize and determine the 3D structure of cellular structures. While many tools exist for the 3D analysis and visualization of crystal or cryo-EM structures little exists for 3D SMLM data, which can provide unique insights but are particularly challenging to analyze in three dimensions especially in a dense cellular context. Results We developed 3DClusterViSu, a method based on 3D Voronoi tessellations that allows local density estimation, segmentation and quantification of 3D SMLM data and visualization of protein clusters within a 3D tool. We show its robust performance on microtubules and histone proteins H2B and CENP-A with distinct spatial distributions. 3DClusterViSu will favor multi-scale and multi-resolution synergies to allow integrating molecular and cellular levels in the analysis of macromolecular complexes. Availability and impementation 3DClusterViSu is available under http://cbi-dev.igbmc.fr/cbi/voronoi3D. Supplementary information Supplementary figures are available at Bioinformatics online.

[1]  David P. Dobkin,et al.  The quickhull algorithm for convex hulls , 1996, TOMS.

[2]  M. Garcia-Parajo,et al.  Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo , 2015, Cell.

[3]  J. Lippincott-Schwartz,et al.  Imaging Intracellular Fluorescent Proteins at Nanometer Resolution , 2006, Science.

[4]  A. Hyman,et al.  Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy. , 2016, Biophysical journal.

[5]  S. Hell,et al.  Two-color nanoscopy of three-dimensional volumes by 4Pi detection of stochastically switched fluorophores , 2011, Nature Methods.

[6]  Alexandre Urzhumtsev,et al.  The integrative role of cryo electron microscopy in molecular and cellular structural biology , 2017, Biology of the cell.

[7]  W. Earnshaw,et al.  The Centromere: Chromatin Foundation for the Kinetochore Machinery , 2014, Developmental cell.

[8]  Suliana Manley,et al.  Simple buffers for 3D STORM microscopy , 2013, Biomedical optics express.

[9]  J. Willemse,et al.  Correlative cryo-fluorescence light microscopy and cryo-electron tomography of Streptomyces. , 2014, Methods in cell biology.

[10]  Astrid Magenau,et al.  Pre-existing clusters of the adaptor Lat do not participate in early T cell signaling events , 2011, Nature Immunology.

[11]  Daniel Choquet,et al.  SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data , 2015, Nature Methods.

[12]  Mark Bates,et al.  Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy , 2008, Science.

[13]  K. Gaus,et al.  Clus-DoC: a combined cluster detection and colocalization analysis for single-molecule localization microscopy data , 2016, Molecular biology of the cell.

[14]  David Baddeley,et al.  Visualization of Localization Microscopy Data , 2010, Microscopy and Microanalysis.

[15]  Yannick Schwab,et al.  Fast and precise targeting of single tumor cells in vivo by multimodal correlative microscopy , 2016, Journal of Cell Science.

[16]  Laurent Cognet,et al.  Identification and super-resolution imaging of ligand-activated receptor dimers in live cells , 2013, Scientific Reports.

[17]  Stephan J Sigrist,et al.  Multi‐colour direct STORM with red emitting carbocyanines , 2012, Biology of the cell.

[18]  Igor Orlov,et al.  ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy , 2016, Scientific Reports.

[19]  S. Dimitrov,et al.  HJURP binds CENP-A via a highly conserved N-terminal domain and mediates its deposition at centromeres , 2010, Proceedings of the National Academy of Sciences.

[20]  M. Sauer,et al.  Photometry unlocks 3D information from 2D localization microscopy data , 2016, Nature Methods.

[21]  Gaël Varoquaux,et al.  The NumPy Array: A Structure for Efficient Numerical Computation , 2011, Computing in Science & Engineering.

[22]  Astrid Magenau,et al.  Quantitative analysis of three-dimensional fluorescence localization microscopy data. , 2013, Biophysical journal.

[23]  P. Verveer,et al.  Coordinate-based colocalization analysis of single-molecule localization microscopy data , 2011, Histochemistry and Cell Biology.

[24]  Yves Lutz,et al.  SharpViSu: integrated analysis and segmentation of super-resolution microscopy data , 2016, Bioinform..

[25]  Franz Aurenhammer,et al.  Voronoi diagrams—a survey of a fundamental geometric data structure , 1991, CSUR.

[26]  R. Margolis,et al.  A 17-kD centromere protein (CENP-A) copurifies with nucleosome core particles and with histones , 1987, The Journal of cell biology.

[27]  John A.G. Briggs,et al.  New hardware and workflows for semi-automated correlative cryo-fluorescence and cryo-electron microscopy/tomography , 2017, Journal of structural biology.

[28]  Peijun Zhang,et al.  Correlative Fluorescence and Electron Microscopy , 2014, Current protocols in cytometry.

[29]  András Horváth,et al.  Correlated confocal and super-resolution imaging by VividSTORM , 2015, Nature Protocols.

[30]  A. D. Gordon,et al.  Interpreting multivariate data , 1982 .

[31]  W. Webb,et al.  Precise nanometer localization analysis for individual fluorescent probes. , 2002, Biophysical journal.

[32]  S. Hell,et al.  Fluorescence nanoscopy by ground-state depletion and single-molecule return , 2008, Nature Methods.

[33]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[34]  Gaël Varoquaux,et al.  Mayavi: 3D Visualization of Scientific Data , 2010, Computing in Science & Engineering.

[35]  K. Grünewald,et al.  Towards correlative super‐resolution fluorescence and electron cryo‐microscopy , 2016, Biology of the cell.

[36]  S. Hess,et al.  Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples , 2008, Nature Methods.

[37]  M. Heilemann,et al.  Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes. , 2008, Angewandte Chemie.

[38]  David J. Williamson,et al.  Bayesian cluster identification in single-molecule localization microscopy data , 2015, Nature Methods.

[39]  M. Dahan,et al.  ViSP: representing single-particle localizations in three dimensions , 2013, Nature Methods.

[40]  Katharina Gaus,et al.  Method for co-cluster analysis in multichannel single-molecule localisation data , 2014, Histochemistry and Cell Biology.