US Based · Spatial Analysis
Spatial Bioinformatics & Analysis
Turn spatial reads into morphology-registered biology. Space Ranger, Xenium Ranger and downstream Seurat and Squidpy workflows, run by our SF Bay Area computational team and delivered in 7 to 10 days.
Spatial Analysis
Scalable spatial bioinformatics
US-based pipelines built for Visium HD, Illumina StrataMap and Xenium data. From automated Space Ranger processing to a dedicated bioinformatician, our tiered models turn spatial matrices into publication-ready 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
Advanced Analysis
Deep-dive spatial profiling for complex tissue architecture.
- Advanced filtering of low-quality bins, contamination and multiplets
- Dimensionality reduction and clustering on filtered data
- tSNE / UMAP plots with cluster information
- General cell type annotation
- Differential expression for clusters and annotated types
- Pathway enrichment analysis
- Group comparison
Best for
Mechanism studies, biomarker localization and translational research
Customized 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
FTE BioFx Model
Dedicated computational support for long-term programs.
- An embedded Signios 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
Figures we deliver
Scoring Heat Map
Delta Distribution
Clonotype Expansion
Cell Type Annotation
Dimensionality Reduction (UMAP / t-SNE) Cluster Plots
Alignment stats
PCA Plot
Correlation Plot
Heatmap
Gene Networks
The Signios advantage
Why choose Signios for spatial analysis
Validated Vendor Pipelines
Space Ranger and Xenium Ranger run to manufacturer specification, so your results are directly comparable to published spatial datasets.
Platform Agnostic
One analysis team across Visium HD, Illumina StrataMap and Xenium. Sequencing-based and imaging-based data handled with the same reporting standard.
Morphology-Registered Output
Every expression map is registered to your own H&E or IF image, so transcripts are interpreted in anatomical context rather than as a coordinate list.
Segmentation & Binning Control
Bin size and cell segmentation are tuned to your tissue rather than left at default, which matters most 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 our Foster City computational team to refine parameters or rebuild figures for a specific journal.
Applications of Spatial Analysis
Our spatial analysis services support a broad range of research applications, including:
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.
Resources & insights
Technical resources
Brochure
Spatial Transcriptomics Brochure
Spatial transcriptomics with Signios Bio: where gene expression meets precision.
BLOG
Choosing the Best Spatial Service for Your Study
Visium HD vs. Xenium Prime vs. Illumina StrataMap — matching platform to study design.
BLOG
Integrating Single-Cell and Spatial Data
Building multimodal maps for translational research.
Frequently asked questions
Everything you need to plan your analysis
Pipelines & platforms
What pipelines do you use for spatial data?
Space Ranger for Visium and Illumina StrataMap, Xenium Ranger for Xenium, with downstream analysis in Seurat and Squidpy. Differential expression uses DESeq2 or the Seurat test appropriate to your design.
Which spatial platforms do you support?
Visium HD (probe-based and 3′), Illumina StrataMap, and 10x Xenium. Sequencing-based and imaging-based data are reported to the same standard.
How do you handle bin size and cell segmentation?
Standard analysis uses the vendor default bin. Customized analysis tunes bin size and segmentation to your tissue, which matters most in dense or heterogeneous sections.
Data & deliverables
How long does analysis take?
7 to 10 days for our standard and advanced packages once data is in hand. Customized workflows are scoped case by case.
What deliverables are included?
Can you analyze data generated elsewhere?
Scope & QC
Can you integrate spatial with single-cell data?
Yes. Spatial data can be deconvolved against a matched single-cell reference to assign cell types with greater confidence, available in the Customized tier.
Do you support non-model species?
How is QC and sample failure handled?
Every project begins with a QC phase evaluating sequencing depth, base quality and capture efficiency. If a section underperforms, our team consults with you before running the main pipeline so you can proceed, filter, or exclude it.
Explore related spatial services
Get started with your analysis
Ready to add spatial context to your study? Contact our team for a technical consultation. We will guide you through assay selection, sample requirements, capture area sizing, and read depth aligned to your analysis goals.
- Volume pricing available on all HD packages
- Data in 3 to 4 weeks, expedited available
- Single cell–scale 2 x 2 µm resolution
- 100% in-house at Foster City, CA