Technology selection guidance, experimental design checkpoints, and starter data resources for spatial transcriptomics. Open any section for a practical overview.
Course 1 · 6–8 Hours · FoundationalUse it as a decision aid, not a fixed buying guide. Access, pricing, and turnaround vary by core facility, service provider, assay configuration, sequencing plan, and analysis support.
| Platform | Class | Spatial Scale | Gene Scope | Best Fit | Access Note |
|---|---|---|---|---|---|
| 10x Visium | Capture-based | 55 µm spots | Whole transcriptome | Broad discovery | Common entry point through cores or service labs |
| 10x Visium HD | Capture-based | Native 2 µm features; often analyzed in larger bins | Whole transcriptome | Higher-resolution discovery | Access and sequencing costs vary sharply by site |
| 10x Xenium | Imaging-based | Subcellular | Targeted panels up to 5,000 genes, plus custom options | Known markers in space | Usually run through a dedicated instrument or service model |
| MERSCOPE Ultra | Imaging-based | Single-cell to subcellular | Custom panels up to about 1,000 genes | Targeted high-resolution imaging | Panel design is part of the study plan |
| Bruker CosMx | Imaging-based | Single-cell to subcellular | Targeted assays and human whole-transcriptome imaging | High-resolution discovery or validation | Capabilities depend on assay type and provider offering |
| Slide-seqV2 | Bead-based | About 10 µm | Whole transcriptome | Advanced academic workflows | Less common as a beginner entry point |
| Stereo-seq | Sequencing-based | 500 nm features with large field-of-view options | Whole transcriptome | Very high spatial granularity | Availability depends on provider and region |
Need broad discovery without selecting genes first? Start with a whole-transcriptome workflow such as Visium or Visium HD.
Need subcellular localization of known genes? Look first at Xenium, MERSCOPE, CosMx, or Stereo-seq.
Working with archived clinical tissue? Check FFPE support early. Visium CytAssist FFPE, Xenium, and CosMx all support FFPE workflows.
Working through a shared core? Ask what platforms the core already runs before comparing internet price estimates.
Platforms such as Visium and Visium HD are strong starting points when you do not yet know which genes matter. They support broad discovery, but standard Visium spots are larger than single cells, and even Visium HD data are often grouped into larger bins during analysis to improve signal strength.
Platforms such as Xenium and MERSCOPE provide much finer spatial detail, including single-cell or subcellular localization, but they depend on panel design. They work best when you already know the cell states, pathways, or markers you want to test.
CosMx is important because it breaks the old idea that whole transcriptome always means lower resolution. Current CosMx workflows include human whole-transcriptome imaging while preserving single-cell and subcellular context.
Choosing a targeted platform too early. If your first question is still “Which genes matter here?”, begin with a whole-transcriptome workflow. Use those results to design a more focused high-resolution follow-up study.
Sequencing depth: Standard Visium fresh-frozen libraries start with a recommended minimum of 50,000 read pairs per tissue-covered spot. Visium FFPE libraries start with 25,000 read pairs per tissue-covered spot. Actual needs depend on assay type, tissue coverage, and study goals.
Tissue work: Sectioning, staining, pathology review, and image handling may sit outside the headline assay quote.
Compute and storage: Spatial projects can include sequencing files, large image files, aligned outputs, and analysis objects that need backup and transfer planning.
Core or service fees: Public pricing examples show wide variation across institutions. A safer planning habit is to confirm sample type, assay availability, sequencing plan, and analysis support before platform selection.
Decide whether your main goal is discovery, validation, or spatial localization of known markers. That usually determines whether you start with a whole-transcriptome workflow or a targeted imaging workflow.
Fresh-frozen: often preferred for broad discovery workflows.
FFPE: essential for many archived clinical samples and supported by current Visium CytAssist FFPE, Xenium, and CosMx workflows.
Three biological replicates per condition can be a practical pilot starting point, but it is not a universal rule. Tissue heterogeneity, effect size, and between-patient variation should drive the final number.
Use positive and negative controls when appropriate, and plan for adjacent histology review or pathologist annotation when morphology matters.
Confirm where raw data, images, aligned outputs, and downstream analysis files will live before data arrive. This prevents late-stage delays and accidental data sprawl.
For human tissue, check consent language, IRB requirements, and any rules around sharing linked image and molecular data before upload or publication.
Good starting point for beginners because the portal includes Visium and Xenium examples and often provides vendor-aligned outputs for learning and benchmarking.
A broad spatial-omics database with unified formatting and interactive analysis modules. Useful when you want cross-platform exploration instead of only one vendor ecosystem.
An early public resource dedicated to curated spatially resolved transcriptomics datasets from published papers. Useful for benchmarking and paper-linked exploration.
A repository of literature and datasets related to spatial transcriptomics, with search, visualization, and analysis support. Helpful when you want Stereo-seq-related examples and broader dataset discovery.
A broad functional-genomics repository. Best when you want datasets tied to specific publications, tissue types, or disease areas, but expect more raw or lightly processed material.
Use this as a reference portal alongside spatial repositories. It is broader than a spatial-only database, but it is useful for reference context and linked single-cell or multi-omic data.
Platform menus, sequencing guidance, and pricing can change. Recheck vendor and core-facility pages before using this guide for purchasing, quoting, or protocol sign-off.