As single-cell omics continue to advance, the field of spatially resolved transcriptomics has emerged with a set of experimental and computational methods to map out the positions of cells and their gene expression profiles in space. Here we summarize current transcriptome-wide and sequencing-based methodologies and their applications in genomics research.

The recent advent of genome-scale imaging has enabled single-cell omics analysis in a spatially resolved manner in intact cells and tissues. These advances allow gene expression profiling of individual cells, and hence in situ identification and spatial mapping of cell types, in complex tissues. The high spatial resolution of these approaches further allows determination of the spatial organizations of the genome and transcriptome inside cells, both of which are key regulatory mechanisms for gene expression.

One major challenge in neuroscience is to gain a systematic understanding of the extraordinary diversity of brain cell types and how they contribute to brain function. Spatially resolved transcriptomics holds unmatched promise in unraveling the organization of brain cell types and their relationship with connectivity, circuit dynamics, behavior and disease. Here we discuss neuroscience applications of various spatially resolved transcriptomics methods, as well as technical challenges that need to be overcome to realize their full potentials.

Nature Methods has crowned spatially resolved transcriptomics Method of the Year 2020.

This study explores the performance of deep-learning models for super-resolution imaging and introduces models that utilize frequency content information in the Fourier domain to improve SIM reconstruction under low-SNR conditions.

This Review describes proximity labeling methods that make use of peroxidases (APEX) or biotin ligases (TurboID, BioID), and their applications to studying protein–protein and protein–nucleic acid interactions in living systems.

EXODUS is a high-speed isolation method for the enrichment of exosome from biological fluids with high purity and yield.

This work presents a sequencing strategy based on unique molecular identifiers that improves long-read consensus sequence accuracy of targeted amplicons as well as shotgun whole-genome fragments.

The iterative Build and Retrieve (BaR) methodology facilitates the solving of cryo-EM structures of multiple membrane (and soluble) proteins simultaneously, including small and low-abundance membrane proteins.

A two-photon miniature microscope with enlarged field of view and axial scanning capabilities has been developed and applied in freely moving mice.

Glycoproteomics is coming of age, thanks to advances in instrumentation, experimental methodologies and computational search algorithms.

Organoids generated by spatially organizing multiple cell types, called assembloids, will enable deeper insights into tissue function.

Computational approaches help us explore complexities of the T cell receptor repertoire.

Method development pushes the limit of completeness of genome sequences.

Single-objective light sheet fluorescence microscopes are driving innovation in volumetric imaging.