Spatial transcriptomics and single-cell RNA sequencing in 2026: overview
Spatial transcriptomics measures gene expression while retaining its location in tissue; single-cell RNA sequencing profiles RNA in individual cells. Together, they reveal both which cell states are present and how those cells are arranged in a tissue’s neighborhoods. This context helps researchers study interactions that bulk measurements can obscure, including immune activity, tumor structure and tissue remodeling. A central challenge is combining detailed molecular profiles with reliable spatial information while managing sparse data, variable sample quality and demanding computational analysis.
Recent work points toward pairing cell-level profiles with tissue context and improving the reliability of analysis. In August 2026, a study of pancreatic cancer combined single-cell RNA sequencing and spatial transcriptomics to characterize exhausted CD8+ T cells. Other August studies proposed DepthDiff, a diffusion-based method for restoring low-depth signals, and stochastic hypergraph co-contrastive learning to address data imputation. Together, these directions show a push to connect cellular states to location while reducing the effects of missing or noisy measurements.
- 1More papers, fewer patents: Publication growth reached 41.3% while patent activity declined 53.0%, pointing to a field whose research output is expanding faster than its recent patenting.
- 2Context meets cell detail: Combining single-cell profiles with spatial measurements helps researchers connect cell states to tissue neighborhoods, as in recent work on exhausted T cells in pancreatic cancer.
- 3Data quality remains central: Methods such as DepthDiff and hypergraph-based imputation target low-depth signals and sparse measurements, keeping analytical reliability a key technical focus.
Top organizations working on spatial transcriptomics and single-cell RNA sequencing
Ranked by Linknovate activity score · last 24 monthsThe activity score adds up the relevance of every patent, publication, grant and news item linking an organization to spatial transcriptomics and single-cell RNA sequencing. Showing 7 of 3,000 organizations.
| # | Organization | Approach | Signals (24 mo) | Momentum | Why it matters |
|---|---|---|---|---|---|
| 1 | 
Sun Yat Sen University
Research · China |
General | PUB 1,202 · NEWS 11 | +50% | Recently, researchers affiliated with the university used single-cell transcriptomics to examine immune and cell-differentiation programs in cancer and endometriosis. |
| 2 | 
Fudan University
Research · China |
General | PUB 1,255 · NEWS 4 | +75% | Recently, researchers affiliated with the university combined single-cell RNA sequencing and proteomics to investigate inflammatory and metabolic changes in dermatomyositis. |
| 3 | 
Southern Medical University
Research · China |
General | PUB 960 | +73% | Recently, researchers affiliated with the university used single-cell analysis to compare keloid samples across populations and investigate cell programs associated with ethnic differences. |
| 4 | SJ
Shanghai Jiao Tong University School Of Medicine
Research |
General | PUB 938 · NEWS 22 | +41% | Recently, researchers affiliated with the medical school used single-cell RNA sequencing to characterize immune-cell heterogeneity in esophageal and temporal-bone cancers. |
| 5 | 
Capital Medical University
Research · China |
General | PUB 861 · NEWS 15 | +66% | Recently, researchers affiliated with the university used single-cell RNA sequencing to map immune states in neonatal sepsis and cellular programs in keloid skin. |
| 6 | CA
Chinese Academy of Medical Seiences & Peking Unian Medical College
Research · China |
General | PUB 874 | +58% | Recently, researchers affiliated with the academy used single-cell RNA sequencing and multi-omics to profile immune-cell states in neonatal sepsis and septic shock. |
| 7 | 
University of California
Research · United States |
General | PUB 909 · NEWS 41 | +5% | Researchers affiliated with the university develop computational methods for single-cell analysis and spatial transcriptomics, including CIPHER, a framework for designing aggregated spatial transcriptomics experiments. |
| 8 | ··Hidden organizationCompany | Approach | PAT 00 · PUB 00 GRANTS 0 · NEWS 00 | +00% | Available to registered users. |
| 9 | ··Hidden organizationCompany | Approach | PAT 00 · PUB 00 GRANTS 0 · NEWS 00 | +00% | Available to registered users. |
| 10 | ··Hidden organizationCompany | Approach | PAT 00 · PUB 00 GRANTS 0 · NEWS 00 | +00% | Available to registered users. |
Startups to watch and leading research centers
Startups to watch 24 total
Singleron Biotechnologies Ltd.ChinaSingleron develops single-cell analysis platforms, including droplet-based workflows for profiling cells and generating transcriptomic data.
VizgenUnited StatesVizgen develops MERFISH, an imaging-based spatial transcriptomics platform that measures many RNA targets in intact tissue while preserving cellular and subcellular location.
Altos Labs Inc.United StatesRecently, researchers affiliated with Altos Labs used single-cell transcriptomics to map age-related changes in primate bone marrow and hematopoietic progenitors.- ··Hidden startupCountryAvailable to registered users, with funding and founding year.
- ··Hidden startupCountryAvailable to registered users, with funding and founding year.
Leading research institutions 2,719 total
- Sun Yat Sen UniversityChinaRecently, researchers affiliated with the university used single-cell transcriptomics to examine immune and cell-differentiation programs in cancer and endometriosis.
- Fudan UniversityChinaRecently, researchers affiliated with the university combined single-cell RNA sequencing and proteomics to investigate inflammatory and metabolic changes in dermatomyositis.
- Southern Medical UniversityChinaRecently, researchers affiliated with the university used single-cell analysis to compare keloid samples across populations and investigate cell programs associated with ethnic differences.
- ··Hidden research institutionCountryAvailable to registered users, with their key researchers.
- ··Hidden research institutionCountryAvailable to registered users, with their key researchers.
Where spatial transcriptomics and single-cell RNA sequencing innovation happens
Share of documents with at least one organization from each country.
Open the interactive map with all 3,000 organizationsMain technical approaches
Last 24 months| Approach | What it is | Documents | Leading organizations |
|---|---|---|---|
| Spatial capture sequencing | Captures RNA from tissue locations for sequencing; it offers broad molecular readout but can blur the identities of nearby cells. | 600 |
National Cancer Institute, University of Wisconsin - Madison, St Jude Childrens Research Hospital |
| Imaging-based spatial profiling | Uses probes and microscopy to detect selected RNA targets in place; it preserves cellular location but depends on the target panel and imaging workflow. | 1,261 |
Harvard University, University of California, Stanford University |
| Droplet-based cell profiling | Partitions cells into droplets for RNA profiling at scale; high throughput comes with dissociation-related loss of tissue context. | 2,744 |
Fudan University, Chinese Academy of Medical Seiences & Peking Unian Medical College, Harvard University |
| Plate-based cell profiling | Processes cells in separate wells, supporting controlled assays and targeted workflows but generally offering less throughput than droplet methods. | 154 |
University of Pennsylvania, Children's Hospital of Philadelphia, Ghent University |
| Single-nucleus profiling | Profiles RNA from isolated nuclei, making it useful for some frozen or hard-to-dissociate tissues but excluding much cytoplasmic RNA. | 1,451 |
University of California, Harvard University, Fudan University |
Emerging trends
Last 12 months vs previous 36 monthsTerms whose frequency in the last 12 months grew the most compared with the previous 36 months.
Funding and investment
Recent funding rounds
FACTS reports $501,352,876 in grants across 607 grants since 2020. The listed fundraising-round data includes entries not clearly specific to this technology, so it should not be read as dedicated investment in the field.
Patent landscape
Top patent holders · last 24 monthsRecent developments
Latest news, duplicates removed- Sep 2026Recovering whole cells from decades-old preserved tissue could make hospital archives a richer source of molecular data. Imagine a volume labeled “Encyclopedia of Human Tissue” resting on a table. Inside might be…SciTechDaily
- Aug 2026Abstract Introduction: Early brain injury (EBI) following subarachnoid hemorrhage (SAH) critically determines neurological outcomes, yet the cellular drivers remain unclear. Methods: To systematically dissect acute…Frontiers in Neuroscience | New and Recent Articles
- Aug 2026Abstract Background: The fetal brain undergoes rapid cellular and structural changes in late gestation, when waves of neurogenesis and gliogenesis shape cortical circuitry. The ventricular zone (VZ), subventricular zone…Frontiers in Neuroscience | New and Recent Articles
- Jul 2026Novogene Europe has expanded its single-cell RNA sequencing capability at its Cambridge Omics Centre. “Single-cell sequencing is helping researchers study complex biological systems with a level of detail that is…Scientist Live
- Month 20XXHidden developmentAvailable to registered users with alerts enabled.
Frequently asked questions about spatial transcriptomics and single-cell RNA sequencing
What companies are working on spatial transcriptomics and single-cell RNA sequencing?
Illumina, 10X Genomics, Genentech and Vizgen are among the named organizations active in this field. Illumina and 10X Genomics appear among the leading patent holders, while Vizgen develops MERFISH, an imaging-based spatial profiling platform. Singleron develops droplet-based single-cell analysis workflows.
Which startups are active in spatial transcriptomics and single-cell RNA sequencing?
Vizgen and Singleron Biotechnologies Ltd. are listed as startups developing relevant platforms. Vizgen develops MERFISH for imaging-based spatial profiling; Singleron develops droplet-based single-cell analysis workflows. Altos Labs is also listed among startups, with recent research using single-cell transcriptomics to study age-related changes in primate bone marrow.
Which universities and research centers lead spatial transcriptomics and single-cell RNA sequencing research?
Fudan University, Sun Yat Sen University and Southern Medical University are among the leading research organizations in the supplied data. Fudan University has 1,260 documents in the window, Sun Yat Sen University has 1,215, and Southern Medical University has 960. Their recent work includes cell-state and immune research across cancer and other diseases.
How much funding has spatial transcriptomics and single-cell RNA sequencing received?
The field has $501,352,876 in reported grant funding across 607 grants since 2020. This figure reflects grants associated with the topic, not a verified total of dedicated commercial investment. The available funding-round entries may include activity not specific to spatial transcriptomics or single-cell RNA sequencing.
Who holds the most spatial transcriptomics and single-cell RNA sequencing patents, and is activity growing?
Illumina leads the listed patent holders with 11 patents, followed by 10X Genomics with 9. Patent activity declined 53.0% in the defined growth window, even as publication activity rose. These figures show a divergence between recent research output and patenting, rather than a broad measure of commercial maturity.
What are the latest developments in spatial transcriptomics and single-cell RNA sequencing?
Recent directions include combining spatial and single-cell methods in pancreatic cancer research and developing tools to address sparse or low-depth data. In August 2026, a study characterized exhausted CD8+ T cells in pancreatic cancer using both methods. DepthDiff and stochastic hypergraph co-contrastive learning are examples of computational approaches targeting signal recovery and imputation.
What are the main approaches, and how do they differ?
Spatial capture sequencing and imaging-based spatial profiling preserve tissue location, while droplet-based, plate-based and single-nucleus profiling focus on RNA from individual cells or nuclei. Capture methods offer broad sequencing readouts but can mix neighboring signals; imaging measures selected targets in place. Cell profiling methods trade tissue context for cell-level characterization, with differences in throughput and sample compatibility.
Which countries lead spatial transcriptomics and single-cell RNA sequencing?
China leads with 40,782 documents, followed by the United States with 36,969 and the United Kingdom with 9,476. Germany and Japan are also among the leading countries in the supplied data. These counts reflect associated documents and indicate strong research activity across multiple regions.
What are the applications of spatial transcriptomics and single-cell RNA sequencing?
Cancer biology, immunology, disease pathology, developmental biology and neuroscience are listed applications. Immunology has 16,664 documents and grew 46.8% in the defined comparison window; cancer biology has 13,064 documents and grew 41.6%. Researchers use these methods to examine cell populations, disease mechanisms and tissue microenvironments.