# Single-Cell & Spatial Omics: State of the Field (October 2026)

Research dossier · v1 · updated 2026-10-30 · 3,177 words · 48 sources · 29 claims · verification: verified

Single-cell and spatial omics now profile tissues at the scale of millions of cells, and perturbation atlases reach about 100 million cells. The central open question is whether learned models of cellular responses beat simple statistical baselines under well-calibrated evaluation, and that question remains contested as of October 2026.

## Contents

- Executive summary
- Background and core concepts
- Timeline of key milestones
- State of the art
  - Dissociation-based single-cell and single-nucleus profiling at atlas scale
  - Imaging-based and sequencing-based spatial transcriptomics
  - Multimodal and spatial multi-omics
  - Computational integration, mapping and spatial inference
  - Perturbation screens and predictive models
  - Quantitative benchmarks
- Open problems and active debates
- Major programs and players
- Outlook: what to watch (near term)
- Key papers
- Glossary

## Sample findings

- A whole-mouse-brain atlas profiled about 7 million cells by scRNA-seq, of which about 4.0 million passed quality control.
- The same atlas spatially profiled about 4.3 million cells using multiplexed error-robust FISH (MERFISH).

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