StrataMap Spatial Transcriptome
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Illumina StrataMap Spatial solution

Build a path to unbiased discovery

Highest spatial discovery power and biological insights at true single-cell resolution

Introducing the StrataMap Spatial solution

The Illumina StrataMap Spatial solution delivers unbiased whole‑transcriptome spatial profiling at true single-cell resolution—combining high sensitivity, large tissue coverage, and seamless integration with Illumina sequencing and analysis to reveal tissue biology in its native context. StrataMap Spatial reveals biology that has not been seen before, with sensitivity, scale, and real-time cellular insights.

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The next frontier of spatial discovery is here

 

 

Discovery without boundaries

StrataMap Spatial eliminates the need to trade off between resolution and breadth of coverage that limits other spatial approaches.

 

No new instruments, no new barriers

With StrataMap Spatial, unlock advanced spatial biology without the high cost and complexity of installing new specialized capital equipment.

 

A more complete view

The large tissue capture area of StrataMap Spatial captures spatial context, cellular detail, and biological complexity in a single experiment instead of multiple fragmented views. ​

 

Comprehensive spatial analysis

StrataMap Spatial is paired with Illumina Connected Multiomics for data visualization and advanced tertiary analysis.

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Discovery without boundaries

See every gene in context without sacrificing resolution

Traditional spatial technologies force researchers to choose between gene coverage and spatial detail. StrataMap Spatial eliminates that tradeoff by delivering true cellular‑level spatial resolution in intact tissue sections for any eukaryotic species. Enabled by a sequencing‑based, poly(A) capture approach and high‑density 1 µm spatial features, the technology preserves precise cellular context. This allows researchers to resolve cell states, interactions, and tissue architecture with clarity.​

Sensitive transcript detection across tissue states

This spatial expression heatmap demonstrates sensitive transcript detection across progressive breast cancer tissue states, from ductal carcinoma in situ (DCIS) with early invasion through high‑grade invasive disease. Consistent, high‑contrast signal across all samples highlights the ability of the StrataMap Spatial solution to capture and resolve spatial gene expression across varying tumor stages, preserving biological gradients and tissue context as disease severity increases.

Consistent transcript detection across sequencing depths

The sequencing saturation curves demonstrate consistent and reliable transcript detection across increasing sequencing depths in breast cancer tissues spanning DCIS and invasive ductal carcinoma (IDC) grades 1–3. As sequencing depth increases, StrataMap Spatial delivers predictable gains in detected molecules and genes per cell, highlighting a robust, scalable workflow that maintains performance across disease states—ensuring confidence that deeper sequencing translates directly into richer biological insight. 

Whole-transcriptome profiling expands gene detection beyond targeted panels

In IDC tissue, next-generation sequencing-based spatial analysis detects a substantially broader set of expressed genes compared to targeted gene panels enabling unbiased transcriptome-wide interrogation.  

Resolving distinct cell populations within the spatial architecture of the tumor microenvironment

This region of interest showcases the ability of StrataMap Spatial to unlock insight by resolving distinct tumor and microenvironment cell populations in their native spatial context. In a high‑grade IDC sample, key tumor and stromal populations are clearly distinguished and precisely localized across the tumor–stroma interface, revealing spatial organization and interactions that drive disease biology. 

Integrated surface architecture and analysis enable cellular resolution spatial transcriptomics 

Cellular-resolution spatial mapping is achieved through continuous 1 μm surface features that preserve spatial detail without signal aggregation across larger regions. In StrataMap Spatial, this resolution reflects the combined contribution of the capture surface architecture, spatially encoded transcript capture, and computational analysis.

Species-agnostic spatial gene expression profiling using poly(A)-based capture

By using poly(A)-based capture, StrataMap Spatial can directly interrogate transcripts from tissue without reliance on species-specific probes. This approach supports spatial gene expression profiling across a wide range of eukaryotic species without assay redesign. 

No new instruments,
no new barriers

A complete spatial workflow, without new capital equipment requirements

Built to integrate seamlessly with standard histology workflows and Illumina sequencing systems already found in many labs around the world, the StrataMap Spatial solution eliminates the need for new specialized capital equipment. The result is a faster path to discovery and broader access to spatial biology across individual labs, shared service facilities, and service providers.​

Step 1

Section and image

Tissue samples are
cryo-sectioned and placed onto the capture surface to preserve native spatial organization.
High‑resolution imaging captures tissue morphology. 

Step 2

Prep

Spatially encoded transcripts are captured from the tissue and converted into sequencing‑ ready libraries. 

Step 3

Sequence

Prepared libraries are sequenced to generate high‑quality spatial gene expression data.

Step 4

Analyze

Analysis translates spatial sequencing data and images into biological insight, revealing cell populations, states, and interactions within the tissue microenvironment.

A more
complete view

Preserve the full biological story across large, intact tissues

Biology does not exist in fragments, and neither should spatial analysis. StrataMap Spatial features a large, flexible capture area that enables researchers to analyze extensive, intact tissue sections within a single experiment—preserving native spatial relationships across cells, regions, and structures. The platform
maintains gradients, microenvironments, and long‑range interactions that are often disrupted or lost with smaller capture formats, resulting in a more complete and faithful view of tissue organization.​

Large capture area supports full tissue profiling

The industry‑leading capture area exceeds that of other spatial transcriptomics platforms. By offering more capture surface per slide, the StrataMap Spatial solution enables profiling of substantially more tissue and cells in a single experiment.

Whole substrate spatial heatmap

This heatmap shows multiple tissue sections across three StrataMap Spatial solution slides. This layout demonstrates the flexibility to accommodate diverse tissue sizes and formats while enabling profiling of a high total number of cells and tissue area per slide. 

Tissue preparation for spatial transcriptomics

Spatial expression heatmaps from a mouse tissue microarray display the large, flexible capture area, enabling simultaneous spatial profiling of multiple tissue types on a single slide. The StrataMap Spatial solution delivers more tissue, more cells, and more biology per slide by accommodating diverse tissues and replicates in one experiment.

A comprehensive
spatial solution

Turn high-resolution data into clear biological insights

The StrataMap Spatial solution pairs its advanced assay with integrated cell segmentation, spatial visualization, and downstream analysis. By helping researchers move seamlessly from raw data to interpretable results and reducing complexity without reducing rigor, the result is faster, more confident interpretation.​

Sequencing data are processed with the DRAGEN spatial transcriptomics pipeline to generate spatially resolved gene expression matrices. This high‑resolution spatial data is then interpreted and visualized in Illumina Connected Multiomics, with tools for clustering, cell-type identification, and exploration of gene expression within tissue context. The platform simplifies complex workflows by enabling real‑time exploration, filtering, and tertiary analyses such as differential expression, marker discovery, and cell typing.​

StrataMap Spatial software workflow

The StrataMap Spatial software workflow seamlessly transforms spatial sequencing data into biological insight. Beginning with tissue images and sequencing output, the workflow integrates spatial mapping, cell type annotation, and gene expression analysis to reveal how cells are organized and interact within their native tissue context. 

Powerful tools for data insights

This figure showcases the Illumina Connected Multiomics (ICM) Spatial Analysis interface, illustrating an intuitive, insight‑driven workflow for exploring spatial biology in a mouse kidney sample. Integrated visualizations spanning spatial domains, cell type relationships, dimensionality reduction, and gene expression patterns enable users to seamlessly connect tissue morphology, cell identity, and molecular signal.

Illumina spatial technology overview

Illumina spatial technology captures polyadenylated RNA transcripts on a substrate. The workflow begins with cryosectioning, H&E staining, and brightfield imaging. RNA is captured on barcoded slides and sequenced, then combined with barcodes and tissue images for spatial mapping. 

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Learn how the Illumina StrataMap Spatial solution can amplify your insights.