Single-cell proteomics is a challenging goal and an area of rapid methods development. This Focus issue highlights the many paths toward high-throughput, high-sensitivity measurements.

SODB is a large-scale platform providing rich data resources, efficient data exporting, and interactive analytical modules for spatial omics research.

Stimulated Raman scattering (SRS) microscopy has the capability to simultaneously visualize the spatial distribution of different biomolecules, but it remains challenging to reach super-resolution. To achieve this goal, a deconvolution algorithm, A-PoD, was developed and combined with SRS microscopy, enabling examination of nanoscopic biomolecular distribution and subcellular metabolic activity in cells and tissues.

Optimal design of spatial transcriptomic experiments allows statistical evaluation of the impact of various biological and technological features on the discovery of cell phenotypes.

Cue achieves versatile and performant structural variant calling and genotyping using a deep-learning approach.

Two miniature microscopes with innovative light paths are described and applied to imaging of juvenile zebra finches and mice.

Femtosecond laser microdissection enables transcriptomic analyses of single neurons based on their phenotype.

A dual line-scanning approach increases imaging speed and reduces illumination levels in Brillouin microscopy, which is demonstrated on spheroids.

A modular architecture for managing and sharing electrophysiology, behavior, colony management and other data has been built to support individual laboratories or large consortia.

A self-inactivating variant of the CVS-N2c rabies virus enables both retrograde viral tracing and transcriptomic analyses, thereby allowing a combination of circuit mapping and molecular studies.

The nanopore community is stepping toward a new frontier of single-molecule protein sequencing. Here, we offer our opinions on the unique potential for this emerging technology, with a focus on single-cell proteomics, and some challenges that must be overcome to realize it.

The development of mass spectrometry-based single-cell proteomics technologies opens unique opportunities to understand the functional crosstalk between cells that drive tumor development.