Development in the STORM.

The recent invention of superresolution microscopy has brought up much excitement in the biological research community. Here, we focus on stochastic optical reconstruction microscopy/photoactivated localization microscopy (STORM/PALM) to discuss the challenges in applying superresolution microscopy to the study of developmental biology, including tissue imaging, sample preparation artifacts, and image interpretation. We also summarize new opportunities that superresolution microscopy could bring to the field of developmental biology.

[1]  K. G. Guruharsha,et al.  The Notch signalling system: recent insights into the complexity of a conserved pathway , 2012, Nature Reviews Genetics.

[2]  S. Hell Far-field optical nanoscopy , 2010 .

[3]  Mike Heilemann,et al.  Super-resolution fluorescence imaging of chromosomal DNA. , 2012, Journal of structural biology.

[4]  G. Krauss Biochemistry of signal transduction and regulation , 1999 .

[5]  Ignacio Izeddin,et al.  PSF shaping using adaptive optics for three-dimensional single-molecule super-resolution imaging and tracking. , 2012, Optics express.

[6]  Mark Bates,et al.  Super-resolution fluorescence microscopy. , 2009, Annual review of biochemistry.

[7]  Christoph Cremer,et al.  Combining FISH with localisation microscopy: Super-resolution imaging of nuclear genome nanostructures , 2010, Chromosome Research.

[8]  T Mustelin Biochemistry of Signal Transduction and Regulation , 2002 .

[9]  C. Ravarani,et al.  Super-resolution imaging of DNA labelled with intercalating dyes. , 2009, Chemphyschem : a European journal of chemical physics and physical chemistry.

[10]  Charles Kervrann,et al.  Condensed Mitotic Chromosome Structure at Nanometer Resolution Using PALM and EGFP- Histones , 2010, PloS one.

[11]  Xiaowei Zhuang,et al.  Coupling between clathrin-dependent endocytic budding and F-BAR-dependent tubulation in a cell-free system , 2010, Nature Cell Biology.

[12]  Sebastian van de Linde,et al.  Live-cell dSTORM with SNAP-tag fusion proteins. , 2011, Nature methods.

[13]  Mike Heilemann,et al.  Three-Dimensional, Tomographic Super-Resolution Fluorescence Imaging of Serially Sectioned Thick Samples , 2012, PloS one.

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

[15]  Ju Lu,et al.  Estimation theoretic measure of resolution for stochastic localization microscopy. , 2012, Physical review letters.

[16]  Hari Shroff,et al.  Single-Molecule Discrimination of Discrete Perisynaptic and Distributed Sites of Actin Filament Assembly within Dendritic Spines , 2010, Neuron.

[17]  E. Ullian,et al.  Afadin, A Ras/Rap Effector That Controls Cadherin Function, Promotes Spine and Excitatory Synapse Density in the Hippocampus , 2012, The Journal of Neuroscience.

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

[19]  K. Rippe,et al.  Dual color localization microscopy of cellular nanostructures , 2009, Biotechnology journal.

[20]  Amanda J Wright,et al.  Adaptive optics for deeper imaging of biological samples. , 2009, Current opinion in biotechnology.

[21]  Stefan W. Hell,et al.  Protein localization in electron micrographs using fluorescence nanoscopy , 2010, Nature Methods.

[22]  Travis J Gould,et al.  Superresolution imaging of multiple fluorescent proteins with highly overlapping emission spectra in living cells. , 2011, Biophysical journal.

[23]  R. Hochstrasser,et al.  Wide-field subdiffraction imaging by accumulated binding of diffusing probes , 2006, Proceedings of the National Academy of Sciences.

[24]  J. Lippincott-Schwartz,et al.  High-density mapping of single-molecule trajectories with photoactivated localization microscopy , 2008, Nature Methods.

[25]  Chenglong Xia,et al.  Super-resolution fluorescence imaging of organelles in live cells with photoswitchable membrane probes , 2012, Proceedings of the National Academy of Sciences.

[26]  A. Diaspro,et al.  Live-cell 3D super-resolution imaging in thick biological samples , 2011, Nature Methods.

[27]  X. Zhuang,et al.  Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells , 2010, Cell.

[28]  X. Zhuang,et al.  Superresolution Imaging of Chemical Synapses in the Brain , 2010, Neuron.

[29]  P. Annibale,et al.  Cell Type-specific 2-Adrenergic Receptor Clusters Identified Using Photoactivated Localization Microscopy Are Not Lipid , 2012 .

[30]  Ned S. Wingreen,et al.  Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy , 2009, PLoS biology.

[31]  Tetsuya Hori,et al.  A super-resolution map of the vertebrate kinetochore , 2010, Proceedings of the National Academy of Sciences.

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

[33]  Mike Heilemann,et al.  Live-cell super-resolution imaging with trimethoprim conjugates , 2010, Nature Methods.

[34]  Keith A. Lidke,et al.  Simultaneous multiple-emitter fitting for single molecule super-resolution imaging , 2011, Biomedical optics express.

[35]  M. Kuroda,et al.  Noncoding RNAs and Intranuclear Positioning in Monoallelic Gene Expression , 2007, Cell.

[36]  J. Sanes,et al.  Chemoaffinity Revisited: Dscams, Protocadherins, and Neural Circuit Assembly , 2010, Cell.

[37]  Shaoqun Zeng,et al.  High-density localization of active molecules using Structured Sparse Model and Bayesian Information Criterion. , 2011, Optics express.

[38]  E. Betzig,et al.  Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics , 2008, Nature Methods.

[39]  S. Holden,et al.  DAOSTORM: an algorithm for high- density super-resolution microscopy , 2011, Nature Methods.

[40]  Christian Eggeling,et al.  Fluorescence Nanoscopy in Whole Cells by Asynchronous Localization of Photoswitching Emitters , 2007, Biophysical journal.

[41]  Christophe Zimmer,et al.  Super-Resolution Dynamic Imaging of Dendritic Spines Using a Low-Affinity Photoconvertible Actin Probe , 2011, PloS one.

[42]  J. Lippincott-Schwartz,et al.  Photoactivatable fluorescent proteins for diffraction-limited and super-resolution imaging. , 2009, Trends in cell biology.

[43]  S. Hell Microscopy and its focal switch , 2008, Nature Methods.

[44]  P. Annibale,et al.  Identification of clustering artifacts in photoactivated localization microscopy , 2011, Nature Methods.

[45]  X. Zhuang,et al.  Whole cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution , 2008, Nature Methods.

[46]  H. Ewers,et al.  A simple, versatile method for GFP-based super-resolution microscopy via nanobodies , 2012, Nature Methods.

[47]  Cherisse R. Loucks,et al.  Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria , 2011, Science.

[48]  Michael W. Davidson,et al.  Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes , 2007, Proceedings of the National Academy of Sciences.

[49]  S. Hell,et al.  Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. , 1994, Optics letters.

[50]  M. Gustafsson Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[51]  M. Gustafsson Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy , 2000, Journal of microscopy.

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

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

[54]  F. Del Bene,et al.  Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy , 2004, Science.

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

[56]  M. Tokunaga,et al.  Highly inclined thin illumination enables clear single-molecule imaging in cells , 2008, Nature Methods.

[57]  S. Hell,et al.  Subdiffraction resolution in far-field fluorescence microscopy. , 1999, Optics letters.

[58]  Xiaowei Zhuang,et al.  Stochastic optical reconstruction microscopy (STORM): a method for superresolution fluorescence imaging. , 2013, Cold Spring Harbor protocols.

[59]  F. Grosveld,et al.  Super-resolution imaging reveals three-dimensional folding dynamics of the &bgr;-globin locus upon gene activation , 2012, Journal of Cell Science.

[60]  J. Lichtman,et al.  3D Multicolor Super-Resolution Imaging Offers Improved Accuracy in Neuron Tracing , 2012, PloS one.

[61]  Daichi Kamiyama,et al.  Endogenous Activation Patterns of Cdc42 GTPase Within Drosophila Embryos , 2009, Science.

[62]  Prabuddha Sengupta,et al.  Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis , 2011, Nature Methods.

[63]  Michael W. Davidson,et al.  Nanoscale architecture of integrin-based cell adhesions , 2010, Nature.

[64]  Christian Eggeling,et al.  Multicolor far-field fluorescence nanoscopy through isolated detection of distinct molecular species. , 2008, Nano letters.

[65]  Atsushi Miyawaki,et al.  Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain , 2011, Nature Neuroscience.

[66]  S. Weiss,et al.  Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI) , 2009, Proceedings of the National Academy of Sciences.

[67]  Lei Zhu,et al.  Faster STORM using compressed sensing , 2012, Nature Methods.

[68]  Dylan T Burnette,et al.  Bleaching/blinking assisted localization microscopy for superresolution imaging using standard fluorescent molecules , 2011, Proceedings of the National Academy of Sciences.

[69]  X. Zhuang,et al.  Evaluation of Fluorophores for Optimal Performance in Localization-Based Super-Resolution Imaging , 2012 .

[70]  Stephen J. Smith,et al.  Array Tomography: A New Tool for Imaging the Molecular Architecture and Ultrastructure of Neural Circuits , 2007, Neuron.

[71]  Andrew G. York,et al.  Confined Activation and Subdiffractive Localization Enables Whole-Cell PALM with Genetically Expressed Probes , 2011, Nature Methods.

[72]  J. Lippincott-Schwartz,et al.  Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure , 2009, Proceedings of the National Academy of Sciences.

[73]  Jianyong Tang,et al.  Three-Dimensional Super-resolution Imaging of Thick Biological Samples , 2009, Microscopy and Microanalysis.

[74]  Thomas Cremer,et al.  The potential of 3D‐FISH and super‐resolution structured illumination microscopy for studies of 3D nuclear architecture , 2012, BioEssays : news and reviews in molecular, cellular and developmental biology.

[75]  P. Annibale,et al.  Quantitative Photo Activated Localization Microscopy: Unraveling the Effects of Photoblinking , 2011, PloS one.

[76]  X. Zhuang,et al.  Statistical deconvolution for superresolution fluorescence microscopy. , 2012, Biophysical journal.

[77]  K. Fujita [Two-photon laser scanning fluorescence microscopy]. , 2007, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.

[78]  Peter Dedecker,et al.  Widely accessible method for superresolution fluorescence imaging of living systems , 2012, Proceedings of the National Academy of Sciences.

[79]  Michael D. Mason,et al.  Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. , 2006, Biophysical journal.

[80]  Hazen P. Babcock,et al.  Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton , 2011, Nature Methods.

[81]  Mark Bates,et al.  Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes , 2007, Science.

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

[83]  X. Zhuang,et al.  Fast three-dimensional super-resolution imaging of live cells , 2011, Nature Methods.

[84]  Samuel T. Hess,et al.  Dynamic clustered distribution of hemagglutinin resolved at 40 nm in living cell membranes discriminates between raft theories , 2007, Proceedings of the National Academy of Sciences.

[85]  Suliana Manley,et al.  Live‐Cell dSTORM of Cellular DNA Based on Direct DNA Labeling , 2012, Chembiochem : a European journal of chemical biology.

[86]  Michael J Rust,et al.  Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) , 2006, Nature Methods.