The spatial organization of post-transcriptional regulation is a fundamental yet difficult to access layer of tissue biology. MicroRNAs (miRNAs) are small RNAs with a key role in post-transcriptional ...

A spatiotemporal transcriptome atlas of whole-human embryos after gastrulation and previously transcriptionally undescribed stages of human development are reported.

In this Review, Liu et al. describe the established and emerging tools for the generation of comprehensive 3D tumour atlases, the analysis of which has the potential to uncover novel biomarkers for ri...

Single-cell transcriptomics is revolutionizing our understanding of cellular diversity, yet comparing transcriptional programs across the tree of life remains challenging. We developed TranscriptForme...

Abstract. The rapid development of updated and new commercially available single-cell transcriptomics platforms provides users with a range of experimental

GigaTIME leverages multimodal AI to generate virtual multiplex immunofluorescence (mIF) profiles from standard H&E slides, enabling comprehensive tumor immune microenvironment modeling across a large ...

A multi-institute, multi-platform initiative generates standard metrics and best practices for spatial transcriptomics analysis.

A multi-institute, multi-platform initiative generates standard metrics and best practices for spatial transcriptomics analysis.

Traditional single-cell technologies are constrained by cellular dimension and throughput scale, in addition to its inability preserve spatial information. With recent innovations, these technologies...

CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.

iSCALE leverages histology and spatial transcriptomics to infer gene expression at super resolution in large tissues.

wellDR-seq allows single-cell whole-genome and transcriptome co-profiling at scale, enabling dissections of complex relationships between copy-number alterations and gene expression that inform our un...

Many single-cell transcriptomics datasets are stored in the HDF5-backed AnnData (H5AD) file format, as popularised by the Python scverse ecosystem. However, accessing these datasets from R, allowing u...

Nature Reviews Genetics, Published online: 21 August 2025; doi:10.1038/s41576-025-00891-6In this Tools of the Trade article, Kellie Wise and Anna Pascual-Reguant introduce STAMP (single-cell transcriptomics analysis and multimodal profiling), which harnesses imaging to measure RNA and/or protein expression in fixed cells or nuclei.

In this Tools of the Trade article, Kellie Wise and Anna Pascual-Reguant introduce STAMP (single-cell transcriptomics analysis and multimodal profiling), which harnesses imaging to measure RNA and/or ...

Cutaneous squamous cell carcinoma (cSCC), basal cell carcinoma (BCC), and melanoma, the three major types of skin cancer, account for over 70% of all cancer cases. Despite their prevalence, the skin c...

No sequencer needed: Imaging based single-cell multiomics

The transformation of normal intestinal epithelium into colorectal cancer (CRC) involves coordinated changes across molecular, cellular, and architectural scales; yet, how these layers integrate remai...

Developed by researchers in the US, Spain, and Australia, STAMP promises to reduce single-cell experiment costs almost 50-fold by eliminating the need for sequencing.

Single-cell transcriptomics analysis and multimodal profiling (STAMP) by imaging enables single-cell analysis of cells in suspension without the need for sequencing. The markedly reduced costs and fle...

The rapid development of updated and new commercially available single-cell transcriptomics platforms provides users with a range of experimental options. Cost, sensitivity, throughput, flexibility, a...

Proseg is a segmentation approach for single-cell spatially resolved transcriptomics data that uses unsupervised probabilistic modeling of the spatial distribution of transcripts to accurately segment...

Advances in AI are transforming scientific discovery, yet spatial biology, a field that deciphers the molecular organization within tissues, remains constrained by labor-intensive workflows. Here, we ...

Recent breakthroughs in spatial transcriptomics technologies have enhanced our understanding of diverse cellular identities, compositions, interactions, spatial organizations, and functions. Yet exist...

Spatial transcriptomics has emerged as a powerful tool to define the cellular structure of diverse tissues. One such method is multiplexed error robust fluorescence in situ hybridization (MERFISH). ME...

The accurate assignment of transcripts to their cells of origin remains the Achilles heel of imaging-based spatial transcriptomics, despite being critical for nearly all downstream analyses. Current c...