Volume 18 Issue 12, December 2021

Sharing, teaching and singing to bring people together on microscopy standards.

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 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.

Rigorous record-keeping and quality control are required to ensure the quality, reproducibility and value of imaging data. The 4DN Initiative and BINA here propose light Microscopy Metadata Specifications that extend the OME Data Model, scale with experimental intent and complexity, and make it possible for scientists to create comprehensive records of imaging experiments.

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.

Technological advances in volume electron microscopy allow imaging and analysis of whole cells at record resolution.

Single-cell GET-seq (scGET-seq) enables the probing of compacted as well as accessible chromatin in single cells, covering a greater portion of the genome, which provides insights into genomic and epigenetic dynamics.

Repair-seq enables efficient profiling of genetic factors involved in DNA double-strand break repair.

A framework to reconstruct tissue architecture from imaging data.

A simple ‘binder/tag’ approach allows tracking of individual protein conformation changes in live cells.

An array of new techniques allow researchers to catalog the chemical contents of a single cell, or even a single organelle.

Software solutions pGlyco3 and StrucGP both aim to better assign the glycan part of a glycopeptide beyond simple glycosyl composition, but they differ in their strategies, their requirement for a glycan library and their applicability to O-glycopeptides.

How a decades-old vaccine for yellow fever may help scientists study the brain connectome.

Comprehensive guidelines and resources to enable accurate reporting for the most common fluorescence light microscopy modalities are reported with the goal of improving microscopy reporting, rigor and reproducibility.

This three-dimensional structural SARS-CoV-2–human interactome web server allows hypothesis-driven exploration of the mechanisms of SARS-CoV-2 pathology and host response.

Micro-Meta App is an intuitive, highly interoperable, open-source software tool designed to facilitate the extraction and collection of relevant microscopy metadata as specified by recent community guidelines.

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.

This work presents biotin-DNA affinity purification (DAP) sequencing, that is, an in vitro, clone-free workflow to profile transcription factor (TF) DNA binding, as well as multiDAP to simultaneously characterize TF DNA binding in multiple bacterial genomes.

SMALT, a base-editing lineage-tracing method, enables whole-organism phylogenetic analyses at single-cell resolution.

pGlyco3 is a glycan-first glycopeptide search engine for the identification and localization of site-specific N- and O-glycopeptides, including glycopeptides with modified glycans.

This manuscript proposes the use of spectral entropy similarity as a measure of similarity for small-molecule mass spectra and the use of a one-bond-difference approach for improving false discovery rates.

Hierarchical phase-contrast tomography (HiP-CT) enables multiscale imaging of any region within an intact human organ down to cellular resolution. HiP-CT of five organ types revealed 3D morphological features in healthy and diseased tissue.

Anterograde transneuronal tracing can be achieved with engineered variants of the yellow fever vaccine YFV-17D. Both monosynaptic and polysynaptic tracing are demonstrated in different circuits of the mouse brain.