FFPE Single-Cell & Spatial Patents: Who Leads, Where Gaps Are 2026
- 63.0% concentration. The top 5 of 45 ranked assignees hold 85 of the 135 records in scope — well over half the field sits with a handful of filers.
- +50% filing growth. Filings rose from 4 in 2021 to 6 in 2024, a three-year rebound after the 2017 peak of 6.
- G01N and C12Q dominate. Material analysis (54.8%) and enzyme/DNA measurement (51.1%) classes cover most records, while C07H and C40B sit under 3% each.
Filing growth compares 2021 (4 records) with 2024 (6) — a three-year span. 2024 is the most recent year we treat as complete: publication lags filing by roughly 18 months, so 2025 onwards are still filling in and any growth rate that ends there would understate the field. Top-5 share is the combined record count of the five largest assignees divided by all 135 records in scope (CR5), not by the ranked leaders only.
What this landscape covers
This landscape tracks 135 published patent families filed between 2015 and 2026 that address formalin-fixed, paraffin-embedded (FFPE) sample compatibility across single-cell and spatial biology workflows — degraded-nucleic-acid recovery, probe-based detection, antigen retrieval, and concordance with fresh-frozen references. The search string combines FFPE-specific terminology with claim-body language covering fragmentation, quality thresholds and morphology preservation, so the scope favours records that engage directly with archival tissue biology rather than general molecular diagnostics.
Filing activity concentrates in material-analysis and enzyme/DNA-measurement classes, with receiving offices led by the United States, WIPO/PCT filings and the European Patent Office. Publication lags filing by roughly 18 months, so 2025 and 2026 figures are still filling in and understate actual filing activity in those years.
Filing trends and technology composition
Trend and classification figures are drawn directly from the 135 records in scope; a record can carry more than one IPC subclass, so class shares sum to more than 100%.
Filing trend, 2017–2026
Filings peaked at 6 in 2017, dipped, and recovered to 6 again by 2024 — a +50% increase over the 2021 figure of 4. The 2025–2026 counts are partial due to publication lag and should not be read as a slowdown.
IPC subclass distribution
G01N (material analysis & testing) and C12Q (enzyme/DNA measurement) each cover more than half of all records, C07K (peptides & proteins) covers over a third, and niche classes like C07H (sugars & nucleic acids) and C40B (combinatorial libraries) sit at 2.2% each — a sign of where claim activity has barely started.
Shares are the percentage of the 135 records in scope. A patent can carry several IPC classes, so the shares add up to more than 100%.
Go deeper on FFPE-Compatible Single-Cell and Spatial Workflows with Eureka
This page is one run against one query. Ask Eureka your own question about ffpe-compatible single-cell and spatial workflows and every answer comes back with the patent numbers behind it.
Try EurekaThe most-cited records in this space
Expansion microscopy compatible and multiplexed in situ hybridization of FFPE tissue sections for spatially resolved transcriptomics
The invention relates to imaging, such as in situ imaging by expansion microscopy, labelling, and analyzing biological samples, such as formalin fixed paraffin embedded (FFPE) cells and tissues, as well as reagents and kits for doing so.Filed by Expansion Technologies, published 2020-11-12 as US20200354782A1.
| # | Publication no. | Patent title | Citations |
|---|---|---|---|
| 1 | US20050272080A1 | Methods of analysis of degraded nucleic acid samples | 139 |
| 2 | US20170283860A1 | Methods and compositions for the removal of aldehyde adducts and crosslinks from biomolecules | 96 |
| 3 | US7374927B2 | Methods of analysis of degraded nucleic acid samples | 92 |
| 4 | US20200354782A1 | Expansion microscopy compatible and multiplexed in situ hybridization of formalin fixed paraffin embedded tis… | 64 |
| 5 | WO2011020529A2 | Antibodies for the detection of integrin complexes in FFPE material | 48 |
| 6 | WO2014139980A1 | Proximity assay for in SITU detection of targets | 46 |
| 7 | WO2016044313A1 | Methods and compositions for the removal of aldehyde adducts and crosslinks from biomolecules | 43 |
| 8 | US20120171699A1 | Antibodies for the detection of integrin complexes in FFPE material | 40 |
| 9 | WO2002046463A2 | Nucleic acid extraction method and kit | 35 |
| 10 | WO2015100459A2 | Biomarker profiles for predicting outcomes of cancer therapy with ERBB3 inhibitors and/or chemotherapies | 20 |
Citation counts are drawn from within this searched corpus and favour older filings; treat them as a signal of influence on the field, not of current commercial relevance.
Each row carries its publication number; clicking a row searches Eureka by that number.
Put your own technology through the same analysis
Eureka on the web
When you want the answer in the next five minutes.
The agent works the prompt against patents and technical literature, citing every source.
Run your analysis now →MCP server & REST API
When it has to run inside your own pipeline.
Patent search, landscape analysis and assignee resolution as MCP tools. Drop them into any agent framework, or call REST directly.
Browse MCP servers →What the numbers mean for strategy
Three patterns stand out once the filing and classification data are read together: concentration at the top, a rebound in recent complete-year filings, and a lopsided technology mix.
The field is not fragmented
The top 5 of 45 ranked assignees account for 85 of the 135 records in scope, and the top 10 extend that to 78.5%. A new entrant is filing into a space where a handful of organisations already hold most of the claim territory, particularly around degraded-nucleic-acid recovery methods.
Recent activity is rebuilding, not fading
After the 2017 peak of 6 filings, activity cooled before climbing back from 4 in 2021 to 6 in 2024. Because publication lags filing by around 18 months, the apparent drop-off in 2025-2026 reflects incomplete data rather than declining interest.
Material analysis and enzyme assays anchor the field
G01N and C12Q together dominate the classification mix, while C07H (sugars & nucleic acids) and C40B (combinatorial libraries) each sit at just 2.2% of records — a much thinner claim layer relative to the core detection and analysis methods.
Eureka can read the same corpus for gaps instead of for coverage: under-claimed branches adjacent to ffpe-compatible single-cell and spatial workflows, with the prior art for and against each one.
Who holds the claim territory
The leader holds 28 records outright, with the fifth-ranked assignee at 7 and the tenth at 3 — a steep drop-off that marks where the long tail of single-filing entrants begins.
One assignee holds a disproportionate share
The top-ranked assignee's 28 records dwarf the fifth-place figure of 7, indicating a filer that has built a defensive perimeter around core FFPE recovery and detection methods rather than a market of evenly matched competitors.
A second tier files steadily but narrowly
Assignees ranked second through fifth collectively make up the balance of the top-5's 63.0% share, suggesting a small set of established players with focused rather than broad portfolios.
Individual inventors cluster into small networks
Ten co-assignee pairs appear in the data, with the strongest overlapping trio sharing 5 records apiece — a pattern more typical of academic or spin-out collaboration than large corporate co-development.
| Assignee | Recent year | YoY |
|---|---|---|
| Merck Patent GmbH | 0 | — |
| Ventana Medical Systems, Inc. | 0 | — |
| Cepheid Inc. | 0 | — |
| Spring Bioscience Corp. | 0 | — |
| Merrimack Pharmaceuticals, Inc. | 0 | — |
| PORTO CONTE RICERCHE SRL | 0 | — |
| Microgenics Corp. | 0 | — |
| WILM CLAUDIA | 0 | — |
Where to take this analysis
The filing and classification data point to specific next steps depending on whether the goal is freedom-to-operate, portfolio strategy or partnership scouting.
Map claim scope on the leading portfolio
With one assignee holding 28 of 135 records, a claim-by-claim review of that portfolio against your own workflow is the fastest way to spot where freedom-to-operate risk actually sits.
Explore assignee portfolios in EurekaTrack the under-claimed branches
C07H, C40B and C07F together cover a small fraction of records; a first-mover claim in these areas faces a thinner prior-art layer than the crowded G01N and C12Q classes.
Run a white-space search in EurekaWatch for filings once 2025-2026 data completes
Because publication lags filing by about 18 months, the true trajectory of 2025-2026 activity will only become visible over the next reporting cycles.
Set up a filing alert in EurekaCommon questions on FFPE workflow patents
The assignee ranking covers 45 companies across the 135 records in scope, and it is heavily front-loaded: the leading assignee holds 28 records, compared with 7 at fifth place and just 3 at tenth. That means the top 5 assignees together account for 63.0% of all records, and the top 10 reach 78.5%. Anyone assessing competitive position in this space should treat the leading handful of filers as the primary reference point rather than the full 45-company list, since most of the remaining assignees hold only a few records each.
Filings grew 50% between 2021 (4 filings) and 2024 (6 filings), following an earlier peak of 6 filings in 2017. The apparent decline in 2025 and 2026 is a data artefact, not a real trend: patent publication typically lags filing by about 18 months, so the most recent one to two years are always undercounted at any point in time. Based on the complete-year data through 2024, the field is rebuilding rather than contracting.
G01N (material analysis and testing) covers 54.8% of the 135 records, and C12Q (measuring and testing involving enzymes or DNA) covers 51.1%, making these the two dominant classes. C07K (peptides and proteins) follows at 36.3% and C12N (microorganisms and genetic engineering) at 25.2%. Because records can carry multiple classes, these figures do not sum to 100%, but together they show the field's centre of gravity is in detection and measurement methods rather than reagent chemistry.
US20200354782A1, filed by Expansion Technologies and published 2020-11-12, covers expansion microscopy combined with multiplexed in situ hybridization specifically adapted for FFPE tissue sections used in spatially resolved transcriptomics. It is the most-cited record in this dataset among the top five most-cited families at 64 citations, indicating substantial downstream engagement by later filers. Teams building expansion-based or multiplexed in situ methods on archival tissue should review its claim scope closely, since it sits at the intersection of two active technical routes: sample expansion and spatial multiplexing.
The classification data points to several under-claimed branches: C07H (sugars and nucleic acids) and C40B (combinatorial chemistry libraries) each account for only 2.2% of the 135 records, and C07F (organo-metallic compounds) sits at 4.4%. These branches sit far below the 54.8% and 51.1% shares held by the dominant G01N and C12Q classes, suggesting thinner prior art around combinatorial probe library design and novel reagent chemistries for degraded-sample recovery. First movers targeting these specific claim spaces face less crowded territory than those filing into core detection methods.
Research FFPE-Compatible Single-Cell and Spatial Workflows in depth with Eureka
Go past this page: query the whole ffpe-compatible single-cell and spatial workflows corpus yourself, in your own scope.
Every answer comes back with patent numbers you can open.
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.