Perspectives

This Perspective describes current and prospective advances in genome engineering made possible with the CRISPR-Cas9 system.

International Cancer Genome Consortium members review and recommend computational approaches for identifying mutations that drive cancer progression from among the many sequence variants present in tumor genomes.

With potential relevance for brain-mapping work, hydrogel-based structures can now be built from within biological tissue to allow subsequent removal of lipids without mechanical disassembly of the tissue. This process creates a tissue-hydrogel hybrid that is physically stable, that preserves fine structure, proteins and nucleic acids, and that is permeable to both visible-spectrum photons and exogenous macromolecules. Here we highlight relevant challenges and opportunities of this approach, especially with regard to integration with complementary methodologies for brain-mapping studies.

Neuronal networks are high-dimensional graphs that are packed into three-dimensional nervous tissue at extremely high density. Comprehensively mapping these networks is therefore a major challenge. Although recent developments in volume electron microscopy imaging have made data acquisition feasible for circuits comprising a few hundreds to a few thousands of neurons, data analysis is massively lagging behind. The aim of this Perspective is to summarize and quantify the challenges for data analysis in cellular-resolution connectomics and describe current solutions involving online crowd-sourcing and machine-learning approaches.

The role of targeted mass spectrometry technology in the field of clinical proteomics is discussed in this Perspective.

This Perspective discusses the registered and publicly available set of Cytoscape plugins to guide potential users to suitable tools.

In this perspective, the authors present the basic features of lens-free computational imaging tools and report performance comparisons with conventional microscopy methods. They also discuss the challenges that these computational on-chip microscopes face for their wide-scale biomedical application.

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.

Presented is an update on the status and current practices of the International Molecular Exchange (IMEx) consortium and on its efforts to create a single nonredundant set of protein interactions curated from the scientific literature.

The Open Microscopy Environment Remote Objects (OMERO) software platform provides a server-based system for managing and analyzing microscopy images and non-image data.

In this Perspective the authors highlight and discuss the artifacts that can arise when using immunolabeling to examine protein localization in cell culture. They call for using both alternative fixation and permeabilization protocols and live-cell imaging of fluorescent protein fusions to reliably study subcellular protein localization.

Authors present workflows for the analysis of metabolism phenotypes in mice and recommend analysis of covariance to asses body composition effects.

In this Perspective the authors discuss strategies for the development of improved fluorescent proteins, with a focus on probes at the red end of the spectrum. They synthesize the literature on chromophore photochemistry and protein structure to identify residues for targeted mutagenesis, and consider improvements in molecular evolution methodologies to enable improved screening for desired probes.