Spatial analysis
Spatial bioinformatics & 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
Analysis packages for spatial data
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.
Standard Analysis
Automated secondary analysis for standard spatial expression studies.
- Space Ranger / Xenium Ranger sequencing QC metrics
- Gene expression matrices and heatmap visualization
- CLOUPE file for Loupe Browser
- Expression registered to your H&E image
Best for standard spatial expression mapping and QC review.
Request this serviceAdvanced Analysis
Deep-dive spatial profiling for complex tissue architecture. Includes everything in Standard, plus:
- Advanced filtering of low-quality bins, contamination and multiplets
- Dimensionality reduction and clustering on filtered data
- t-SNE / UMAP plots with cluster information
- General cell-type annotation
- Differential expression for clusters and annotated types
- Pathway enrichment analysis and group comparison
Best for mechanism studies, biomarker localization and translational research.
Request this serviceCustomized Analysis
Tailored spatial workflows built around your study parameters.
- Custom bin size and cell segmentation tuning
- Region-of-interest and neighborhood analysis
- Cell-type deconvolution against a reference
- Integration with matched single-cell datasets
Best for specialized designs, non-model species and multimodal integration.
Request this serviceFTE BioFx Model
Dedicated computational support for long-term programs.
- An embedded bioinformatician
- Iterative data mining and custom tool development
- Journal-specific figure preparation
- Scalable capacity without new hires
Best for pharma and biotech teams needing sustained analytical capacity.
Request this serviceThe Gateway advantage
Why choose us for spatial analysis
Validated vendor pipelines
Space Ranger and Xenium Ranger run to manufacturer specification, so results compare directly to published spatial datasets.
Platform agnostic
One analysis team across Visium HD, Illumina StrataMap and Xenium — sequencing-based and imaging-based data reported to the same standard.
Morphology-registered output
Every expression map is registered to your own H&E or IF image, so transcripts are interpreted in anatomical context.
Segmentation & binning control
Bin size and cell segmentation tuned to your tissue rather than left at default — critical in dense or heterogeneous sections.
Single-cell integration ready
Spatial data can be deconvolved against a matched single-cell reference to assign cell types with greater confidence.
Scientist-to-scientist support
Work directly with the computational team to refine parameters or rebuild figures for a specific journal.
Analysis workflow
From spatial reads to mapped biology
Step 1
Consultation
Define analysis goals, assay, capture-area sizing and read depth.
Step 2
Data ingestion
Spatial data accepted from any facility via secure transfer, with QC confirmed before processing.
Step 3
Vendor pipelines
Space Ranger or Xenium Ranger processing to manufacturer specification.
Step 4
Downstream analysis
Seurat and Squidpy workflows — clustering, annotation, DE and neighborhood analysis per package.
Step 5
Delivery & reporting
Matrices, browser files, QC report and PDF figures registered to your tissue image.
Beyond the FASTQ
Figures we deliver
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
Where this service delivers
Tumor microenvironment
Locate immune infiltration, stromal boundaries and tumor margins in situ.
Neuroanatomical mapping
Resolve cortical layers and regional expression gradients across intact brain sections.
Biomarker localization
Confirm where a candidate marker is expressed — not just whether it is present.
Neighborhood analysis
Quantify which cell types sit together to infer signaling and interaction patterns.
Treatment response
Compare treated and control sections to see which compartments respond.
Multimodal integration
Combine spatial expression with single-cell, proteomic or epigenomic data.
FAQs
Plan your project
Resources & insights
Go deeper
Explore related spatial services
Spatial & analysis services
Get started with your analysis
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.
- Volume pricing on all HD packages
- Data in 3–4 weeks, expedited available
- Single-cell-scale 2×2 µm resolution
- Fully in-house computational team
Ready to launch your study?
Share your samples and goals — a doctoral-level scientist responds within one business day with a study plan and competing blind quotes.
- Expert-guided study design & service matching
- Competitive quotes, adaptable turnaround times
- End-to-end bioinformatics & reporting
- Run by accredited facilities across the nationwide network
Administered by Syntax of Life Private Limited
Request a quote