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Spatial analysis
Turn spatial reads into morphology-registered biology — Space Ranger, Xenium Ranger and downstream Seurat and Squidpy workflows delivered in 7 to 10 days.
0–10 days
standard & advanced analysis
0×2 µm
single-cell-scale resolution
0 platforms
Visium HD, StrataMap & Xenium
Scalable spatial bioinformatics
Pipelines built for Visium HD, Illumina StrataMap and Xenium — from automated Space Ranger processing to a dedicated bioinformatician, turning spatial matrices into biology registered to your own H&E image.
Automated secondary analysis for standard spatial expression studies.
Best for standard spatial expression mapping and QC review.
Request this serviceDeep-dive spatial profiling for complex tissue architecture. Includes everything in Standard, plus:
Best for mechanism studies, biomarker localization and translational research.
Request this serviceTailored spatial workflows built around your study parameters.
Best for specialized designs, non-model species and multimodal integration.
Request this serviceDedicated computational support for long-term programs.
Best for pharma and biotech teams needing sustained analytical capacity.
Request this serviceThe Gateway advantage
Space Ranger and Xenium Ranger run to manufacturer specification, so results compare directly to published spatial datasets.
One analysis team across Visium HD, Illumina StrataMap and Xenium — sequencing-based and imaging-based data reported to the same standard.
Every expression map is registered to your own H&E or IF image, so transcripts are interpreted in anatomical context.
Bin size and cell segmentation tuned to your tissue rather than left at default — critical in dense or heterogeneous sections.
Spatial data can be deconvolved against a matched single-cell reference to assign cell types with greater confidence.
Work directly with the computational team to refine parameters or rebuild figures for a specific journal.
Analysis workflow
Step 1
Define analysis goals, assay, capture-area sizing and read depth.
Step 2
Spatial data accepted from any facility via secure transfer, with QC confirmed before processing.
Step 3
Space Ranger or Xenium Ranger processing to manufacturer specification.
Step 4
Seurat and Squidpy workflows — clustering, annotation, DE and neighborhood analysis per package.
Step 5
Matrices, browser files, QC report and PDF figures registered to your tissue image.
Beyond the FASTQ
Spatial analysis typically completes in 7–10 days; volume pricing available on all HD packages.
Deliverables include
Alignment stats
PCA plots
Correlation plots
Heatmaps
Gene networks
Scoring heat maps
Alignment stats
PCA plots
Correlation plots
Heatmaps
Gene networks
Scoring heat maps
Delta distribution
Clonotype expansion
Cell-type annotation
UMAP / t-SNE cluster plots
H&E-registered expression maps
Neighborhood analysis
Delta distribution
Clonotype expansion
Cell-type annotation
UMAP / t-SNE cluster plots
H&E-registered expression maps
Neighborhood analysis
Figures & files delivered with every project — hover to pause
Applications
Locate immune infiltration, stromal boundaries and tumor margins in situ.
Resolve cortical layers and regional expression gradients across intact brain sections.
Confirm where a candidate marker is expressed — not just whether it is present.
Quantify which cell types sit together to infer signaling and interaction patterns.
Compare treated and control sections to see which compartments respond.
Combine spatial expression with single-cell, proteomic or epigenomic data.
FAQs
Resources & insights
Explore related spatial services
Ready to add spatial context to your study? Contact the team for a technical consultation — assay selection, sample requirements, capture-area sizing and read depth aligned to your goals.
Share your samples and goals — a doctoral-level scientist responds within one business day with a study plan and competing blind quotes.
Administered by Syntax of Life Private Limited
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