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An exceptionally large-scale project aimed at assigning function to all protein-coding genes in the human genome is reported on page 721 by Neumann et al.¹. Here are two complementary views on the experimental design and analysis, and on how useful the findings will be to cell biologists.

Image repositories are growing. Their potential impact is huge; they require support and proper funding.

This Perspective provides a roadmap toward globally federated open data resources for bioimaging data.

OME’s next-generation file format (OME-NGFF) provides a cloud-native complement to OME-TIFF and HDF5 for storing and accessing bioimaging data at scale and works toward the goal of findable, accessible, interoperable and reusable bioimaging data.

Efforts to generate nanoscale-resolution images of cell interiors have gained ground through the development and refinement of a microscopy method. The data sets are publicly available as resources for further discoveries.

Protein immunofluorescence imaging and affinity purification–mass spectrometry are combined to create a unified map of human cell architecture across scales, which the authors call the multi-scale integrated cell (MuSIC).

Using a previously developed method, Singer and co-workers have now labeled RNA transcripts and quantitatively measured the synthesis of RNA in living cells. They find that only a small fraction of the RNA polymerases that bind the promoter actually produce messenger RNA. They also observed much faster elongation than previously reported, along with frequent long pauses.

With vast increases in biological data generation, mechanisms for data storage and analysis have become limiting. A data structure, semantically typed data hypercubes (SDCubes), that combines hierarchical data format version 5 (HDF5) and extensible markup language (XML) file formats, now permits the flexible storage, annotation and retrieval of large and heterogenous datasets.

PP2A-B56 regulates the stability of kinetochore-microtubule attachments by dephosphorylating several kinetochore proteins. Porter et al. identify Bod1 as a specific inhibitor of PP2A-B56 phosphatase activity and show that this activity is required for proper chromosome alignment during mitosis.

This report describes the outcomes of the Data Management Challenges in 3D Electron Microscopy workshop. Key topics discussed include data models, validation and raw-data archiving. The meeting participants agreed that the EMDataBank should take the lead in addressing these issues, and concrete action points were agreed upon that will have a substantial impact on the accessibility of three-dimensional EM data in biology and medicine.

Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.

The dynamic localization of PLK1 to kinetochores is required for faithful chromosome segregation. Peter, Sumara and colleagues demonstrate that a KHL22-containing E3 ligase mediates degradation-independent removal of PLK1 from kinetochores to ensure satisfaction of the spindle assembly checkpoint and proper mitotic progression.

Imaging technologies are used throughout the life and biomedical sciences to understand mechanisms in biology and diagnosis and therapy in animal and human medicine. We present criteria for globally applicable guidelines for open image data tools and resources for the rapidly developing fields of biological and biomedical imaging.

The European Lead Factory combines assets and experience from major pharma with innovation and agility of academia and SMEs in a collaborative platform to expand access to high-throughput screening. With many successes heading towards the clinic, the organization is broadening its approach to screening and partnering.

The community-driven initiative Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMi) wants to improve reproducibility for light microscopy image data through quality control (QC) management of instruments and images. It aims for a common set of QC guidelines for hardware calibration and image acquisition, management and analysis.

We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community.

This Resource describes the Image Data Resource (IDR), a prototype online system for biological image data that links experimental and analytic data across multiple data sets and promotes image data sharing and reanalysis.

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

The imminent release of tissue atlases combining multichannel microscopy with single-cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards to guide data deposition, curation and release. We describe a Minimum Information about Highly Multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and for other microscopy data to highly multiplexed tissue images and traditional histology.

Public data archives are the backbone of modern biological research. Biomolecular archives are well established, but bioimaging resources lag behind them. The technology required for imaging archives is now available, thus enabling the creation of the first public bioimage datasets. We present the rationale for the construction of bioimage archives and their associated databases to underpin the next revolution in bioinformatics discovery.