Innovation in biological microscopy: Current status and future directions

The current revolution in biological microscopy stems from the realisation that advances in optics and computational tools and automation make the modern microscope an instrument that can access all scales relevant to modern biology – from individual molecules all the way to whole tissues and organisms and from single snapshots to time‐lapse recordings sampling from milliseconds to days. As these and more new technologies appear, the challenges of delivering them to the community grows as well. I discuss some of these challenges, and the examples where openly shared technology have made an impact on the field.

[1]  A. Gamal,et al.  Miniaturized integration of a fluorescence microscope , 2011, Nature Methods.

[2]  Anne E Carpenter,et al.  CellProfiler: image analysis software for identifying and quantifying cell phenotypes , 2006, Genome Biology.

[3]  D. Agard,et al.  The use of a charge-coupled device for quantitative optical microscopy of biological structures. , 1987, Science.

[4]  N. Cohen,et al.  Open innovation networks between academia and industry: an imperative for breakthrough therapies , 2009, Nature Medicine.

[5]  Ambuj K. Singh,et al.  Bisque: a platform for bioimage analysis and management , 2009, Bioinform..

[6]  J. Ploem,et al.  The use of a vertical illuminator with interchangeable dichroic mirrors for fluorescence microscopy with incidental light. , 1967, Zeitschrift fur wissenschaftliche Mikroskopie und mikroskopische Technik.

[7]  P. Schwille,et al.  Fluorescence correlation spectroscopy in living cells , 2007, Nature Methods.

[8]  F. Helmchen,et al.  Ultra-compact fiber-optic two-photon microscope for functional fluorescence imaging in vivo. , 2008, Optics express.

[9]  J. Murray,et al.  Methods for imaging thick specimens: confocal microscopy, deconvolution, and structured illumination. , 2011, Cold Spring Harbor protocols.

[10]  David A. Agard,et al.  Three-dimensional architecture of a polytene nucleus , 1983, Nature.

[11]  H. Leonhardt,et al.  A guide to super-resolution fluorescence microscopy , 2010, The Journal of cell biology.

[12]  Lani F. Wu,et al.  Multidimensional Drug Profiling By Automated Microscopy , 2004, Science.

[13]  R. Durbin,et al.  Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes , 2010, Nature.

[14]  Anastasia Khvorova,et al.  Corrigendum: 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets , 2007, Nature Methods.

[15]  Winfried Wiegraebe,et al.  Fluorescence correlation spectroscopy as tool for high-content-screening in yeast (HCS-FCS) , 2011, BiOS.

[16]  G. Danuser,et al.  Quantitative fluorescent speckle microscopy of cytoskeleton dynamics. , 2006, Annual review of biophysics and biomolecular structure.

[17]  K. Eliceiri,et al.  Bioimage informatics for experimental biology. , 2009, Annual review of biophysics.

[18]  Maryann E Martone,et al.  The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. , 2008, Journal of structural biology.

[19]  Michael D. Abràmoff,et al.  Image processing with ImageJ , 2004 .

[20]  D. Agard Optical sectioning microscopy: cellular architecture in three dimensions. , 1984, Annual review of biophysics and bioengineering.

[21]  Hidemi Sato,et al.  Deoxyribonucleic Acid Arrangement in Living Sperm , 2008 .

[22]  Robert R McLeod,et al.  GRIN lens and lens array fabrication with diffusion-driven photopolymer. , 2008, Optics letters.

[23]  G van Meer,et al.  Sorting of sphingolipids in epithelial (Madin-Darby canine kidney) cells , 1987, The Journal of cell biology.

[24]  Bernd Fischer,et al.  CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging , 2010, Nature Methods.

[25]  Terry S. Yoo,et al.  Insight into Images: Principles and Practice for Segmentation, Registration, and Image Analysis , 2004 .

[26]  E. Hill,et al.  Announcing the JCB DataViewer, a browser-based application for viewing original image files , 2008, The Journal of Cell Biology.

[27]  F. Zernike How I discovered phase contrast. , 1955, Science.

[28]  Anastasia Khvorova,et al.  3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets , 2006, Nature Methods.

[29]  Mehmet Fatih Yanik,et al.  Large-scale in vivo femtosecond laser neurosurgery screen reveals small-molecule enhancer of regeneration , 2010, Proceedings of the National Academy of Sciences.

[30]  D. Kleinfeld,et al.  In vivo dendritic calcium dynamics in neocortical pyramidal neurons , 1997, Nature.

[31]  A. Mehta,et al.  Multiphoton endoscopy: optical design and application to in vivo imaging of mammalian hippocampal neurons , 2003, Conference on Lasers and Electro-Optics, 2003. CLEO '03..

[32]  Philipp J. Keller,et al.  Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy , 2008, Science.

[33]  Robert M Zucker,et al.  Evaluation of confocal microscopy system performance. , 2001, Methods in molecular biology.

[34]  Jason R Swedlow,et al.  Measuring tubulin content in Toxoplasma gondii: A comparison of laser-scanning confocal and wide-field fluorescence microscopy , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[35]  L. Lim,et al.  Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. , 2006, RNA.

[36]  D. Sabatini,et al.  Microarrays of cells expressing defined cDNAs , 2001, Nature.

[37]  S INOUE,et al.  [Polarization optical studies of the mitotic spindle. I. The demonstration of spindle fibers in living cells]. , 1953, Chromosoma.

[38]  M. Fordham,et al.  An evaluation of confocal versus conventional imaging of biological structures by fluorescence light microscopy , 1987, The Journal of cell biology.

[39]  Julie Moss,et al.  EMAGE mouse embryo spatial gene expression database: 2014 update , 2013, Nucleic Acids Res..

[40]  Aabid Shariff,et al.  Automated Image Analysis for High-Content Screening and Analysis , 2010, Journal of biomolecular screening.

[41]  M. Davidson,et al.  Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination , 2011, Nature Methods.

[42]  H. Erfle,et al.  High-throughput RNAi screening by time-lapse imaging of live human cells , 2006, Nature Methods.

[43]  C. Conrad,et al.  Automatic identification of subcellular phenotypes on human cell arrays. , 2004, Genome research.

[44]  Erik Brauner,et al.  Informatics and Quantitative Analysis in Biological Imaging , 2003, Science.

[45]  C. Conrad,et al.  Automated microscopy for high-content RNAi screening , 2010, The Journal of cell biology.

[46]  Jan Ellenberg,et al.  Micropilot: automation of fluorescence microscopy–based imaging for systems biology , 2011, Nature Methods.

[47]  J. Swedlow,et al.  Evaluating performance in three-dimensional fluorescence microscopy , 2007, Journal of microscopy.

[48]  Anne-Marie Girard,et al.  Quality assurance testing for modern optical imaging systems. , 2011, Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada.

[49]  A. Zvyagin Multiphoton endoscopy , 2007 .

[50]  T Wilson,et al.  The theory of the direct‐view confocal microscope , 1981, Journal of microscopy.