Spatial Transcriptomics Patents: Who Leads, Where the Gaps Are 2026
- 67.0% of all 176 records sit with just five assignees — filing here is concentrated, not fragmented, and the top ten hold 90.3%.
- Filing peaked in 2022 at 42 records and has declined since; 2026 shows only 3, though the most recent year is always undercounted due to publication lag.
- C12Q covers 90.3% of records while image recognition (G06V, 8.5%) and bioinformatics (G16B, 7.4%) remain comparatively thin claim territory.
A field defined early by a small number of founding claims
Spatial transcriptomics and spatial omics patenting sits at the intersection of molecular biology, imaging, and computation: methods for reading nucleic acid sequences in situ, in place within intact tissue, alongside the image registration and panel-design work needed to make that readout usable at scale. The search scope here spans 176 published records filed against classifications covering enzymatic and DNA-based measurement, material analysis, and image or bioinformatics processing — a combination that reflects how tightly the wet-lab chemistry and the software stack are now claimed together.
The filing curve rose steadily through the technology's early commercialisation window and peaked in 2022 before declining, a pattern consistent with a field where the foundational in situ sequencing chemistry was staked out early and subsequent filings increasingly compete for narrower claim space around panel size, capture efficiency and tissue handling rather than the core method itself.
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Filing trends and technology composition
The dataset covers 176 published records filed between 2015 and mid-2026 against a search scope combining spatial transcriptomics terminology with technical qualifiers such as spatial resolution, capture efficiency and image registration.
A peak year, then a pullback
Annual filings rose from 8 in 2017 to a peak of 42 in 2022, then declined through 2026 (3 records, partial year). Because publication typically lags filing by roughly 18 months, the last one to two years of any such curve will always look thinner than the underlying filing activity actually was.
Claim territory concentrated in nucleic acid measurement
C12Q (enzyme- and DNA-based measurement) appears in 90.3% of the 176 records in scope, with C12N (genetic engineering) a distant second at 34.1%. Image recognition (G06V, 8.5%), bioinformatics (G16B, 7.4%) and healthcare informatics (G16H, 5.7%) are present but far less saturated — these are the classes where a record can carry several codes at once, so the shares add to more than 100% by design.
Shares are the percentage of the 176 records in scope. A patent can carry several IPC classes, so the shares add up to more than 100%.
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This page is one run against one query. Ask Eureka your own question about spatial transcriptomics and spatial omics and every answer comes back with the patent numbers behind it.
Try EurekaThe most-cited records anchor the in situ sequencing method itself
Scalable Distributed Processing Software for Next-Generation in Situ Sequencing (US20240257912A1)
Methods, systems, and devices, including computer programs encoded on a computer storage medium, are provided for processing next-generation in situ sequencing data for nucleic acids in cells in tissue. In particular, cloud-based scalable data processing software for volumetric in situ sequencing is provided.Filed by The Board of Trustees of the Leland Stanford Junior University, published 2024-08-01.
| # | Publication no. | Patent title | Citations |
|---|---|---|---|
| 1 | WO2005082098A2 | Polony fluorescent in SITU sequencing beads | 454 |
| 2 | US10059990B2 | In situ nucleic acid sequencing of expanded biological samples | 443 |
| 3 | US7425431B2 | Polony fluorescent in situ sequencing beads | 365 |
| 4 | US20070087362A1 | Polony fluorescent in situ sequencing beads | 333 |
| 5 | WO2018045181A1 | Methods of generating libraries of nucleic acid sequences for detection via fluorescent in situ sequencing | 248 |
| 6 | WO2020160044A1 | In-SITU spatial transcriptomics | 146 |
| 7 | US20220106633A1 | Spatial transcriptomics for antigen-receptors | 141 |
| 8 | US20210095331A1 | Deterministic barcoding for spatial omics sequencing | 140 |
| 9 | US20230047782A1 | Quantitative and automated permeabilization performance evaluation for spatial transcriptomics | 104 |
| 10 | US20160304952A1 | In situ nucleic acid sequencing of expanded biological samples | 102 |
Citation counts favour older records within any searched corpus — read them as a signal of foundational influence, not of which claims are most commercially active today.
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Three figures from this dataset matter more than the raw count of 176 records: how concentrated the ownership is, where the technology mix is thin, and what the citation record says about which claims are foundational versus incremental.
Five organisations hold most of the claim territory
The top five assignees combined account for 118 of the 176 records in scope, and the top ten extend that to 90.3%. A field this concentrated at the top, with a leader well ahead of fifth place, means new entrants are more likely to find open space in adjacent method claims than in the core in situ sequencing chemistry itself.
Filing has cooled since its 2022 peak
Annual filings climbed from 8 in 2017 to 42 in 2022, then declined toward 3 by 2026. Recent-year assignee activity shows several of the leading filers at zero or near-zero in the latest year, though this partly reflects the roughly 18-month lag between filing and publication rather than a genuine stop in R&D.
Imaging and bioinformatics claims remain thin relative to the chemistry
C12Q measurement and testing claims dominate at 90.3% of records, but image recognition (G06V) and bioinformatics (G16B) sit at 8.5% and 7.4% respectively. Given how central image registration and computational panel design are to making spatial omics workflows scale, this gap between wet-lab and software claim density is worth watching.
Eureka can read the same corpus for gaps instead of for coverage: under-claimed branches adjacent to spatial transcriptomics and spatial omics, with the prior art for and against each one.
A leader well ahead of a long tail of single- and few-filing entrants
The assignee ranking returned by this dataset covers 46 companies and institutions, from a leader with 44 records down to entrants with a handful of filings each. Ownership is dominated by a mix of core sequencing-platform companies and the university and research-institute labs that co-invented the underlying chemistry.
One assignee sits well clear of the field
The leading assignee holds 44 of the 176 records in scope, roughly four times the fifth-place count of 11. That gap suggests a platform company that filed early and continued to build a defensive perimeter around its core method, rather than a field where leadership rotates year to year.
Beyond the top ten, filing thins out quickly
The top ten assignees already account for 90.3% of all records, leaving the remaining 36 ranked organisations sharing the rest. Many of these hold only a small number of filings each — worth checking individually before assuming they represent active competitive programmes rather than one-off academic filings.
Founding-era institutions still co-file together
Several of the strongest co-assignee pairs link major research institutions that co-developed early in situ sequencing methods, with pair counts in the high single digits. This pattern is typical of technology that originated in academic labs before being licensed or spun into a commercial platform.
| Assignee | Recent year | YoY |
|---|---|---|
| Illumina, Inc. | 1 | — |
| The Board of Trustees of the Leland Stanford Junior University | 1 | 0% |
| 10x Genomics, Inc. | 0 | -100% |
| President and Fellows of Harvard College | 0 | — |
| Massachusetts Institute of Technology | 0 | — |
| The Broad Institute, Inc. | 0 | — |
| The Regents of the University of California | 0 | — |
| MILTENYI BIOTEC BV & CO KG | 0 | — |
Where to take this analysis
The figures here describe the shape of the field as published; the next step is usually to test a specific claim or a specific gap against the full-text record.
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Take a candidate method — say, an image registration or panel-design approach — and check it against the full claim language of the top-cited records before committing engineering time.
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Recent-year momentum figures here are thinned by publication lag; a live monitor on the leading assignees will surface new filings as they publish rather than waiting for the next dataset refresh.
Set up monitoring in EurekaMap the white space branches in more depth
The under-claimed sub-areas flagged here (image registration, panel optimisation, bioinformatics pipelines) deserve a dedicated search rather than a single IPC-level read.
Build a custom search in EurekaCommon questions about spatial transcriptomics patents
Within this 176-record dataset, one assignee leads with 44 records, well ahead of the fifth-ranked entrant at 11. The leading holders are a mix of sequencing-platform companies and the university and research-institute labs that co-developed the underlying in situ sequencing chemistry. The top five assignees combined account for 67.0% of all 176 records, so the field is concentrated rather than evenly spread across many small filers.
Filing rose from 8 records in 2017 to a peak of 42 in 2022, then declined toward 3 by 2026. That does not necessarily mean R&D activity has stopped — publication lags filing by roughly 18 months, so the most recent one to two years in any such trend will always look artificially thin. Recent-year assignee-level momentum figures in this dataset show most leading filers at low or zero counts in the latest year, consistent with that lag.
C12Q, the classification covering enzyme- and DNA-based measurement and testing, appears in 90.3% of the 176 records in scope, making it by far the dominant claim territory. C12N (genetic engineering) follows at 34.1%, with material analysis (G01N), image recognition (G06V) and bioinformatics (G16B) present at lower shares. Because a single record can carry multiple classification codes, these percentages sum to more than 100%.
The technology composition data points to image recognition and bioinformatics as comparatively under-claimed relative to the core sequencing chemistry — G06V sits at 8.5% of records and G16B at 7.4%, versus 90.3% for the core measurement classification. Sub-areas like automated panel-size optimisation, multiplexed image registration and cross-platform bioinformatics pipelines show lower claim density and may offer more room for a first, well-drafted claim than the heavily occupied core method space.
US20240257912A1, filed by The Board of Trustees of the Leland Stanford Junior University and published 2024-08-01, covers cloud-based scalable software for processing next-generation in situ sequencing data, including volumetric in situ sequencing workflows. It sits in the computational-processing layer of the spatial omics stack rather than the wet-lab chemistry itself. Anyone building distributed or cloud-based processing pipelines for in situ sequencing data should review its specific claim language before assuming their architecture is clear of it.
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Disclaimer. This page is generated from Patsnap Eureka data drawn from a limited snapshot of global patent and scientific-literature records, and is provided for general information and reference only.
Patent data carries inherent limitations: recent filings (typically the most recent 18–24 months) are under-counted due to standard publication lag; counts may be reported at either a patent-family or a patent-record basis and are not always directly comparable; classification, applicant-name, and citation data may contain errors, duplicates, or omissions; and the underlying search query defines and constrains the scope shown. As a result, the analysis may be incomplete or inaccurate and may not reflect the full technology landscape.
Nothing on this page constitutes an exhaustive prior-art, novelty, freedom-to-operate, or validity search, nor does it constitute legal, financial, investment, or professional advice, and it should not be relied upon as such. Any patent, commercial, or strategic decision should be verified independently and reviewed with qualified patent, legal, and domain professionals. Patsnap makes no warranties, express or implied, as to the accuracy, completeness, or fitness for any particular purpose of the information presented.
Machine translation. Assignee and organisation names originally recorded in Chinese, Japanese or Korean have been rendered into English by an AI translation step so that the tables stay readable. These renderings are best-effort and may not match a company’s registered English name; the original name is what the underlying patent record carries, and it is what any Eureka query launched from this page uses.