Nature Methods Contents: July 2012 Volume 9 pp 627 - 763

Advertisement Ribo-Zero™ Magnetic Kits Ribo-Zero kits remove >99% of rRNA from intact or degraded total RNA samples. The kits are suitable for a wide variety of mammalian, plant, and bacterial RNA samples. Learn more: http://www.epicentre.com/ribozero TABLE OF CONTENTS July 2012 Volume 9, Issue 7 In This Issue Focus Editorial This Month Correspondence Research Highlights Methods in Brief Tools in Brief Technology Feature News and Views Commentaries Historical Commentary Perspectives Review Brief Communications Articles Advertisement Ion Torrent PGM Certified Service Provider Use IMGM's professional semiconductor sequencing to accelerate your research. We offer: • Personal project manager • Free project consultation • Assay development • Target enrichment • Library preparation • PGM sequencing • Expert bioinformatics • Informative reports Our expertise - Your success! Click here for details More genomic services Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement The Genova Nano; Jenway's first 3 in 1 spectrophotometer measures small sample volumes as low as 0.5µl with a high degree of accuracy, reproducibility and speed. Its ability to measure small sample volumes, conserves precious samples, reduces the need for dilutions and eliminates the requirement for cuvettes. Click here for further details.   Advertisement Have you seen the new spectroscopyNOW.com and separationNOW.com websites? Keep ahead with global news, research and education in your area of analytical science. Explore new content, features and design, plus register today and customise your view to see only site content that is of interest to you.   In This Issue Top In This Issue Focus Top Focus on Bioimage Informatics Focus issue: July 2012 Volume 9 No 7 Contents Editorial This Month Correspondence Commentary Historical Commentary Perspectives Review Brief Communications Article Editorial Top Focus on Bioimage Informatics The quest for quantitative microscopy   p627 doi:10.1038/nmeth.2102 With the aid of informatics, microscopy is in the midst of a crucial evolution into a more quantitative and powerful technique. This Month Top Focus on Bioimage Informatics The author file: Robert F. Murphy   p629 Monya Baker doi:10.1038/nmeth.2088 Creating algorithms to turn images into cell models Points of view: Representing genomic structural variation   p631 Cydney Nielsen and Bang Wong doi:10.1038/nmeth.2018 Techniques for displaying relations between distant genomic positions. Correspondence Top Focus on Bioimage Informatics OMERO.searcher: content-based image search for microscope images   pp633 - 634 Baek Hwan Cho, Ivan Cao-Berg, Jennifer Ann Bakal and Robert F Murphy doi:10.1038/nmeth.2086 Focus on Bioimage Informatics SimuCell: a flexible framework for creating synthetic microscopy images   pp634 - 635 Satwik Rajaram, Benjamin Pavie, Nicholas E F Hac, Steven J Altschuler and Lani F Wu doi:10.1038/nmeth.2096 Focus on Bioimage Informatics PhenoRipper: software for rapidly profiling microscopy images   pp635 - 637 Satwik Rajaram, Benjamin Pavie, Lani F Wu and Steven J Altschuler doi:10.1038/nmeth.2097 Focus on Bioimage Informatics Annotated high-throughput microscopy image sets for validation   p637 Vebjorn Ljosa, Katherine L Sokolnicki and Anne E Carpenter doi:10.1038/nmeth.2083 Research Highlights Top Secrets of RNA granules   p639 A surprising hydrogel formation promises insight on prions and RNA transport. DNA nanoLEGOlogy   pp640 - 641 Researchers design a simple 'shake & bake' method for the assembly of complex nanostructures from interlocking DNA tiles. Sorting out epigenetic states   pp640 - 641 A nanofluidic device can sort single DNA molecules based on their epigenetic marks. Shaping the waves   p642 An optical compensation technique enables deeper, crisper two-photon microscopy. Taming stem cell heterogeneity   p645 Human embryonic stem cells are screened with a panel of antibodies to identify cellular subsets that may correspond to early human progenitor cell populations. The sixth base and counting   p646 Enzymatic glycosylation and oxidation of methylated DNA together with high-throughput sequencing allows genome-wide base-resolution of 5-hydroxymethyl cytosine distribution. Methods JOBS of the week Post-Doc Position – Detection and determination of phytopathogenic bacteria using methods of molecular biology 1) Faculty of Agriculture University of South Bohemia in Ceské Budejovice and Institute of Plant Molecular Biology (IPMB) of2) Biology Centre of the Academy of Sciences of the Czech Republic in Ceské Budejovice Research worker of applied physical methods Institute of Theoretical and Applied Mechanics ASCR, v. v. i. Stochastic methods for geophysics MINES ParisTech Ph.D. position on Methods and algorithms for data processing of the imaging Fourier transform spectrometer GLORIA Karlsruhe Institute of Technology (KIT) - Helmholtz Association More Science jobs from Methods EVENT T2012 AACR/ASCO Workshop: Methods in Clinical Cancer Research 28th July - 3rd August 2012 US More science events from Methods in Brief Top Membrane proteins in 3D | The synaptic transcriptome | Exciting fluorescence with luminescence | Virtual swimmers Tools in Brief Top Super-resolution FlAsH | Assemble-on-a-chip | Metallic electron microscopy | Functional glycoarrays Technology Feature Top Mass spectrometry for chromatin biology   pp649 - 652 Monya Baker doi:10.1038/nmeth.2081 To discover new histone marks and interactions, researchers turn to the sophisticated instruments of proteomics. News and Views Top Faster and more versatile tools for super-resolution fluorescence microscopy   pp655 - 656 Alex Small doi:10.1038/nmeth.2079 Two methods for estimating fluorophore positions provide useful new options to researchers performing either single-particle tracking or super-resolution imaging. See also: Brief Communication by Zhu et al. | Brief Communication by Parthasarathy Omnidirectional microscopy   pp656 - 657 Michael Weber and Jan Huisken doi:10.1038/nmeth.2022 In toto imaging of living embryos has now become much faster. Light-sheet illumination and fluorescence detection with four objective lenses provide complete coverage of large samples in a snap. See also: Article by Tomer et al. | Brief Communication by Krzic et al. Commentaries Top Focus on Bioimage Informatics Why bioimage informatics matters   pp659 - 660 Gene Myers doi:10.1038/nmeth.2024 Driven by the importance of spatial and physical factors in cellular processes and the size and complexity of modern image data, computational analysis of biological imagery has become a vital emerging sub-discipline of bioinformatics and computer vision. Focus on Bioimage Informatics Current challenges in open-source bioimage informatics   pp661 - 665 Albert Cardona and Pavel Tomancak doi:10.1038/nmeth.2082 We discuss the advantages and challenges of the open-source strategy in biological image analysis and argue that its full impact will not be realized without better support and recognition of software engineers' contributions to the biological sciences and more support of this development model from funders and institutions. Focus on Bioimage Informatics A call for bioimaging software usability   pp666 - 670 Anne E Carpenter, Lee Kamentsky and Kevin W Eliceiri doi:10.1038/nmeth.2073 Bioimaging software developed in a research setting often is not widely used by the scientific community. We suggest that, to maximize both the public's and researchers' investments, usability should be a more highly valued goal. We describe specific characteristics of usability toward which bioimaging software projects should aim. Historical Commentary Top Focus on Bioimage Informatics NIH Image to ImageJ: 25 years of image analysis   pp671 - 675 Caroline A Schneider, Wayne S Rasband and Kevin W Eliceiri doi:10.1038/nmeth.2089 For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the analysis of scientific images. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects. Perspectives Top Focus on Bioimage Informatics Fiji: an open-source platform for biological-image analysis   pp676 - 682 Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid, Jean-Yves Tinevez, Daniel James White, Volker Hartenstein, Kevin Eliceiri, Pavel Tomancak and Albert Cardona doi:10.1038/nmeth.2019 Presented is an overview of the image-analysis software platform Fiji, a distribution of ImageJ that updates the underlying ImageJ architecture and adds modern software design elements to expand the capabilities of the platform and facilitate collaboration between biologists and computer scientists. Focus on Bioimage Informatics BioImageXD: an open, general-purpose and high-throughput image-processing platform   pp683 - 689 Pasi Kankaanpää, Lassi Paavolainen, Silja Tiitta, Mikko Karjalainen, Joacim Päivärinne, Jonna Nieminen, Varpu Marjomäki, Jyrki Heino and Daniel J White doi:10.1038/nmeth.2047 Focus on Bioimage Informatics Icy: an open bioimage informatics platform for extended reproducible research   pp690 - 696 Fabrice de Chaumont, Stéphane Dallongeville, Nicolas Chenouard, Nicolas Hervé, Sorin Pop, Thomas Provoost, Vannary Meas-Yedid, Praveen Pankajakshan, Timothée Lecomte, Yoann Le Montagner, Thibault Lagache, Alexandre Dufour and Jean-Christophe Olivo-Marin doi:10.1038/nmeth.2075 Icy is a collaborative platform for biological image analysis that extends reproducible research principles by facilitating and stimulating the contribution and sharing of algorithm-based tools and protocols between researchers. Review Top Focus on Bioimage Informatics Biological imaging software tools   pp697 - 710 Kevin W Eliceiri, Michael R Berthold, Ilya G Goldberg, Luis Ibáñez, B S Manjunath, Maryann E Martone, Robert F Murphy, Hanchuan Peng, Anne L Plant, Badrinath Roysam, Nico Stuurmann, Jason R Swedlow, Pavel Tomancak and Anne E Carpenter doi:10.1038/nmeth.2084 Representative members of the bioimage informatics community review the computational steps and some of the primary software tools available to biologists who are acquiring and analyzing microscopy-based digital image data, with a focus on open-source options. Brief Communications Top Focus on Bioimage Informatics Unsupervised modeling of cell morphology dynamics for time-lapse microscopy   pp711 - 713 Qing Zhong, Alberto Giovanni Busetto, Juan P Fededa, Joachim M Buhmann and Daniel W Gerlich doi:10.1038/nmeth.2046 The authors present a bioinformatic method for the accurate unsupervised classification of time-lapse images. This method should enable reproducible and unbiased annotation of large-scale image data sets. Focus on Bioimage Informatics An image analysis toolbox for high-throughput C. elegans assays   pp714 - 716 Carolina Wählby, Lee Kamentsky, Zihan H Liu, Tammy Riklin-Raviv, Annie L Conery, Eyleen J O'Rourke, Katherine L Sokolnicki, Orane Visvikis, Vebjorn Ljosa, Javier E Irazoqui, Polina Golland, Gary Ruvkun, Frederick M Ausubel and Anne E Carpenter doi:10.1038/nmeth.1984 The freely available WormToolbox enables high-throughput image analysis of a variety of phenotypes of Caenorhabditis elegans in liquid culture and should prove useful for image-based screens. Focus on Bioimage Informatics Elastic volume reconstruction from series of ultra-thin microscopy sections   pp717 - 720 Stephan Saalfeld, Richard Fetter, Albert Cardona and Pavel Tomancak doi:10.1038/nmeth.2072 The authors describe a method for realigning images from serially sectioned biological specimens that minimizes the effect of artificial deformations in the alignment by applying global elastic constraints. The method is applied to transmission electron microscopy and array tomography image series and is made available through the Fiji platform. Focus on Bioimage Informatics Faster STORM using compressed sensing   pp721 - 723 Lei Zhu, Wei Zhang, Daniel Elnatan and Bo Huang doi:10.1038/nmeth.1978 Global optimization of single-molecule localizations using compressed sensing allows stochastic optical reconstruction microscopy (STORM) at high molecular densities and live cell super-resolution imaging with a temporal resolution of 3 seconds. See also: News and Views by Small Focus on Bioimage Informatics Rapid, accurate particle tracking by calculation of radial symmetry centers   pp724 - 726 Raghuveer Parthasarathy doi:10.1038/nmeth.2071 An analytically exact approach that determines the radial symmetry center of the image of any radially symmetric particle allows faster localization than iterative methods while also giving localization accuracies approaching theoretical limits. See also: News and Views by Small Rational design of true monomeric and bright photoactivatable fluorescent proteins   pp727 - 729 Mingshu Zhang, Hao Chang, Yongdeng Zhang, Junwei Yu, Lijie Wu, Wei Ji, Juanjuan Chen, Bei Liu, Jingze Lu, Yingfang Liu, Junlong Zhang, Pingyong Xu and Tao Xu doi:10.1038/nmeth.2021 Structure determination followed by targeted engineering of the popular photoactivatable fluorescent protein monomeric (m)Eos2 yields mEos3 versions that are more monomeric and less disruptive in protein fusions and also exhibit higher labeling density, brightness and other beneficial properties. Multiview light-sheet microscope for rapid in toto imaging   pp730 - 733 Uros Krzic, Stefan Gunther, Timothy E Saunders, Sebastian J Streichan and Lars Hufnagel doi:10.1038/nmeth.2064 A selective-plane illumination microscope with two illumination and two detection objectives rapidly records four three-dimensional images of an entire developing fly embryo and processes them into a single high-content image in real time. This allows for cell tracking and quantification of cell shape changes across the embryo. A related paper by Tomer et al. is also in this issue. See also: News and Views by Weber & Huisken Advertisement BD Pharmingen™ transcription factor buffer set This newly optimized fixation and permeabilization buffer system improves sensitivity for many transcription factors including FoxP3, RORyt, T-bet, Bcl-6, and others. Request a free sample and get connected to high-sensitivity detection of intracellular and intranuclear proteins with flow cytometry. bdbiosciences.com/go/tfbuffer   Articles Top Focus on Bioimage Informatics ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains   pp735 - 742 Olaf Ronneberger, Kun Liu, Meta Rath, Dominik Rueβ, Thomas Mueller, Henrik Skibbe, Benjamin Drayer, Thorsten Schmidt, Alida Filippi, Roland Nitschke, Thomas Brox, Hans Burkhardt and Wolfgang Driever doi:10.1038/nmeth.2076 An imaging and registration framework called Virtual Brain Explorer for Zebrafish (ViBE-Z) allows mapping of gene expression patterns and anatomical structures in the zebrafish larval brain. ViBE-Z is provided via a web interface and contains software for image processing, data sets from several developmental stages and a brain atlas. Single-cell systems biology by super-resolution imaging and combinatorial labeling   pp743 - 748 Eric Lubeck and Long Cai doi:10.1038/nmeth.2069 Super-resolution microscopy of fluorescently labeled oligonucleotides bound to individual mRNA transcripts is used for highly multiplexed imaging and quantification of transcripts in single cells. The method is used to profile transcripts from 32 stress-response genes in single yeast cells in response to extracellular stress. Resolution doubling in live, multicellular organisms via multifocal structured illumination microscopy   pp749 - 754 Andrew G York, Sapun H Parekh, Damian Dalle Nogare, Robert S Fischer, Kelsey Temprine, Marina Mione, Ajay B Chitnis, Christian A Combs and Hari Shroff doi:10.1038/nmeth.2025 Structured illumination using multifocal patterned illumination via a digital micromirror device integrated into a conventional wide-field microscope, followed by digital processing, allows resolution-doubled three-dimensional imaging of live organisms with two-color capability. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy   pp755 - 763 Raju Tomer, Khaled Khairy, Fernando Amat and Philipp J Keller doi:10.1038/nmeth.2062 Simultaneous multiview light-sheet microscopy using two illumination and two detection arms with one- or two-photon illumination is coupled to a fast data acquisition framework and analysis pipeline for quantitative imaging and tracking of individual cells and the developing nervous system throughout a living fly embryo. A related paper by Krzic et al. is also in this issue. See also: News and Views by Weber & Huisken Top Advertisement Nature Methods Focus on Bioimage Informatics The need to extract quantitative data from increasingly large and complex microscopy datasets requires sophisticated image acquisition and analysis methods and software. This focus issue discusses these tools and the challenges and opportunities in the field. 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