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

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 ...

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...

No sequencer needed: Imaging based single-cell multiomics

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...

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...

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.

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...

ezSingleCell is an interactive and user-friendly application for the analysis of single-cell and spatial omics data, without the need for programming expertise. Here, authors integrated top-performing...

AbstractSummary. DamID sequencing is a technique to map the genome-wide interaction of a protein with DNA. Damsel is the first Bioconductor package to prov

AbstractSummary. This study introduces easySCF, a tool designed to enhance the interoperability of single-cell data between the two major bioinformatics pl

Abstract. Spatially Resolved Transcriptomics (SRT) serves as a cornerstone in biomedical research, revealing the heterogeneity of tissue microenvironments.

Scientists reflect on insights from the Human Cell Atlas.

Spatially resolved transcriptomics methods can now profile the entire transcriptome, at full organism scale with nanometre resolution. Analysis frameworks that can efficiently and intuitively process....

Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we ...

Python package for Probe set selection for targeted spatial transcriptomics. - theislab/spapros

Perturb-seq enabled the profiling of transcriptional effects of genetic perturbations in single cells but lacks the ability to examine the impact on tissue environments. We present Perturb-DBiT for si...

Patho-DBiT enables spatial profiling of a range of RNA species (i.e., mRNA, microRNA, tRNA, splicing isoform, etc.) all at once in clinical formalin-fixed paraffin-embedded tissue with high sensitivit...

Spatially resolved transcriptomics methods can now profile the entire transcriptome, at full organism scale with nanometre resolution. Analysis frameworks that can efficiently and intuitively process....