Focus
Focus on Bioimage Informatics
Explosive growth in the size and complexity of microscopy-based imaging data and the need to extract more quantitative data from it increasingly requires sophisticated image acquisition and analysis methods and software tools. A collection of articles discusses the role of bioimage informatics in microscopy, specific tools that are available, and the challenges and opportunities in the field.
Editorial
Focus on Bioimage Informatics
The quest for quantitative microscopy
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.
Abstract - | Full Text - The quest for quantitative microscopy | PDF (54 KB) - The quest for quantitative microscopy
This Month
Focus on Bioimage Informatics
The Author File: Robert F. Murphy
Monya Baker
doi:10.1038/nmeth.2088
Creating algorithms to turn images into cell models.
Abstract - | Full Text - Gene-editing nucleases | PDF (105 KB)
Correspondence
Focus on Bioimage Informatics
OMERO.searcher: content-based image search for microscope images
Baek Hwan Cho, Ivan Cao-Berg, Jennifer Ann Bakal & Robert F Murphy
doi:10.1038/nmeth.2086
Full Text - OMERO.searcher: content-based image search for microscope images | PDF (136 KB) | Supplementary information - OMERO.searcher: content-based image search for microscope images
Focus on Bioimage Informatics
SimuCell: a flexible framework for creating synthetic microscopy images -
Satwik Rajaram, Benjamin Pavie, Nicholas E F Hac, Steven J Altschuler & Lani F Wu
doi:10.1038/nmeth.2096
Full Text - SimuCell: a flexible framework for creating synthetic microscopy images | PDF (213 KB) | Supplementary information -SimuCell: a flexible framework for creating synthetic microscopy images
Focus on Bioimage Informatics
PhenoRipper: software for rapidly profiling microscopy images -
Satwik Rajaram, Benjamin Pavie, Lani F Wu & Steven J Altschuler
doi:10.1038/nmeth.2097
Full Text - PhenoRipper: software for rapidly profiling microscopy images | PDF (352 KB)| Supplementary information - PhenoRipper: software for rapidly profiling microscopy images
Focus on Bioimage Informatics
Annotated high-throughput microscopy image sets for validation -
Vebjorn Ljosa, Katherine L Sokolnicki & Anne E Carpenter
doi:10.1038/nmeth.2083
Full Text - Annotated high-throughput microscopy image sets for validation | PDF (73 KB)
Commentary
Focus on Bioimage Informatics
Why bioimage informatics matters -
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.
Abstract - | Full Text - Why bioimage informatics matters | PDF (79KB)
Focus on Bioimage Informatics
Current challenges in open-source bioimage informatics -
Albert Cardona & 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.
Abstract - | Full Text - Current challenges in open-source bioimage informatics | PDF (403 KB)
Focus on Bioimage Informatics
A call for bioimaging software usability-
Anne E Carpenter, Lee Kamentsky & 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.
Abstract - | Full Text - A call for bioimaging software usability | PDF (197 KB)
Historical Commentary
Focus on Bioimage Informatics
NIH Image to ImageJ: 25 years of image analysis -
Caroline A Schneider, Wayne S Rasband & 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.
Abstract - | Full Text - NIH Image to ImageJ: 25 years of image analysis | PDF (330 KB)
Perspectives
Focus on Bioimage Informatics
Fiji: an open-source platform for biological-image analysis -
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 & 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.
Abstract - | Full Text - Fiji: an open-source platform for biological-image analysis | PDF (1,284 KB)
Focus on Bioimage Informatics
BioImageXD: an open, general-purpose and high-throughput image-processing platform -
Pasi Kankaanpää, Lassi Paavolainen, Silja Tiitta, Mikko Karjalainen, Joacim Päivärinne, Jonna Nieminen, Varpu Marjomäki, Jyrki Heino & Daniel J White
doi:10.1038/nmeth.2047
Described is BioImageXD, a simple, user-friendly, open-source platform for biological image analysis. The authors outline their design criteria and how BioImageXD meets them, and demonstrate BioImageXD performance in a study of integrin clustering.
Abstract - | Full Text - BioImageXD: an open, general-purpose and high-throughput image-processing platform | PDF (1,383 KB)
Focus on Bioimage Informatics
Icy: an open bioimage informatics platform for extended reproducible research -
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 & 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.
Abstract - | Full Text - Light-based electrophysiology | PDF (1,248 KB)
Review
Focus on Bioimage Informatics
Biological imaging software tools -
Kevin W Eliceiri, Michael R Berthold, Ilya G Goldberg, Luis Ibàñez, B S Manjunath, Maryann E Martone, Robert F Murphy, Hanchuan Peng, Anne L Plant, Badrinath Roysam, Nico Stuurmann, Jason R Swedlow, Pavel Tomancak & 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.
Abstract - | Full Text - Biological imaging software tools | PDF (1,574 KB)
Brief Communications
Focus on Bioimage Informatics
Unsupervised modeling of cell morphology dynamics for time-lapse microscopy -
Qing Zhong, Alberto Giovanni Busetto, Juan P Fededa, Joachim M Buhmann & 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.
Abstract - | Full Text - Unsupervised modeling of cell morphology dynamics for time-lapse microscopy | PDF (1,048 KB)
Focus on Bioimage Informatics
An image analysis toolbox for high-throughput C. elegans assays -
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 & 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.
Abstract - | Full Text - An image analysis toolbox for high-throughput C. elegans assays | PDF (470 KB)
Focus on Bioimage Informatics
Elastic volume reconstruction from series of ultra-thin microscopy sections -
Stephan Saalfeld, Richard Fetter, Albert Cardona & 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.
Abstract - | Full Text - Elastic volume reconstruction from series of ultra-thin microscopy sections | PDF (1,146 KB)
Focus on Bioimage Informatics
Faster STORM using compressed sensing -
Lei Zhu, Wei Zhang, Daniel Elnatan & 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.
Abstract - | Full Text - Faster STORM using compressed sensing | PDF (481 KB)
Focus on Bioimage Informatics
Rapid, accurate particle tracking by calculation of radial symmetry centers -
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.
Abstract - | Full Text - Rapid, accurate particle tracking by calculation of radial symmetry centers | PDF (666 KB)
Article
Focus on Bioimage Informatics
ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains -
Olaf Ronneberger, Kun Liu, Meta Rath, Dominik Rueβ, Thomas Mueller, Henrik Skibbe, Benjamin Drayer, Thorsten Schmidt, Alida Filippi, Roland Nitschke, Thomas Brox, Hans Burkhardt & 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.
Abstract - | Full Text - Rapid, accurate particle tracking by calculation of radial symmetry centers | PDF (2,2422 KB)