Nature Methods welcomes manuscript submissions that describe new technology, tool and methodology developments across the spectrum of basic biology research. Here, we clarify our scope and highlight some areas of interest.

A deep learning algorithm maps out the continuous conformational changes of flexible protein molecules from single-particle cryo-electron microscopy images, allowing the visualization of the conformational landscape of a protein with improved resolution of its moving parts.

A new mutagenesis platform enables the fast, cost-efficient and automatable production of defined multi-site sequence variants for a wide range of applications. Demonstrations of this method included the generation of SARS-CoV-2 spike gene variants, DNA fragments for large-scale genome engineering, and adeno-associated virus 2 (AAV2) cap genes with improved packaging capacity.

Photoselective sequencing is a new method for genomic and epigenomic profiling within specific regions of a biological specimen that are chosen using light microscopy. This combination of spatial and sequencing information preserves the connections between genomic and environmental properties and deepens our understanding of structure–function relationships in cells and tissues.

This paper proposes two new anisotropy metrics—the Fourier shell occupancy and the Bingham test—that can be used to understand the quality of cryogenic electron microscopy maps.

CAMPA (Conditional Autoencoder for Multiplexed Pixel Analysis) learns representations of molecular pixel profiles from multiplexed images that can be clustered to quantify subcellular landmarks and capture interpretable cellular phenotypes.

SIMBA learns a co-embedding space of single cells and multiple features such as genes, chromatin-accessible regions and transcription-factor-binding sequences, boosting the performances of various analyses of cellular diversity and regulation.

MISAR-seq combines spatial-ATAC-seq and RNA-seq for spatial profiling of both chromatin accessibility and gene expression, as demonstrated in the developing mouse brain.

The miniature RNA-guided endonuclease IscB and its ωRNA were engineered for efficient gene editing in mammalian cells. Fusions of ‘enIscB’ to T5 exonuclease and cytosine or adenosine deaminase yield versatile tools for genome engineering.

This updated analysis of the Cell Tracking Challenge explores how algorithms for cell segmentation and tracking in both 2D and 3D have advanced in recent years, pointing users to high-performing tools and developers to open challenges.

As they pursue their puzzles of interest, scientists are inventive caretakers of the organisms in their keep, especially the young.

A microscope objective inspired by the Schmidt telescope offers a large field of view, high numerical aperture, long working distance and compatibility with all homogeneous immersion media for versatile bioimaging.