Volume 9 Issue 7, July 2012

Creating algorithms to turn images into cell models

Techniques for displaying relations between distant genomic positions.

A surprising hydrogel formation promises insight on prions and RNA transport.

Researchers design a simple 'shake & bake' method for the assembly of complex nanostructures from interlocking DNA tiles.

A nanofluidic device can sort single DNA molecules based on their epigenetic marks.

An optical compensation technique enables deeper, crisper two-photon microscopy.

Human embryonic stem cells are screened with a panel of antibodies to identify cellular subsets that may correspond to early human progenitor cell populations.

Enzymatic glycosylation and oxidation of methylated DNA together with high-throughput sequencing allows genome-wide base-resolution of 5-hydroxymethyl cytosine distribution.

To discover new histone marks and interactions, researchers turn to the sophisticated instruments of proteomics.

Two methods for estimating fluorophore positions provide useful new options to researchers performing either single-particle tracking or super-resolution imaging.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.