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Spatial Single-Cell Multi-omics

Unifying spatial context with multi-modal molecular profiles.

mysimulator teamUpdated June 2026≈ 3 min read▶ Open the simulation

Platforms

Spatial transcriptomics + proteomics

In situ sequencing and imaging mass spectrometry

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Integration

Joint embeddings, spot deconvolution, and cell–cell communication inference.

Examples

Example: Tumor Microenvironment Atlas

Design panels and imaging protocol.

Integrate single-cell references.

Map niches and therapeutic targets.

Frequently asked questions

How to align modalities?

Register images and harmonize feature spaces.

How to validate?

Orthogonal assays and perturbation experiments.

Throughput vs resolution?

Balance based on tissue and biological question.

Batch effects?

Correct across sessions and platforms.

Data volumes?

Adopt scalable storage and processing pipelines.

Standards?

Emerging schemas; document metadata thoroughly.

Segmentation?

Use models tuned to tissue and imaging modality.

Cell–cell interactions?

Combine proximity and ligand–receptor models.

Visualization?

Interactive maps with layers and annotations.

Ethics?

Consent, de-identification, and data governance.

Try it live

Everything above runs in your browser — open Spatial Single-Cell Multi-omics: Tissue Niche Explorer and change the parameters while it is running. Nothing is installed, nothing is uploaded, the whole model lives in one tab.

▶ Open Spatial Single-Cell Multi-omics: Tissue Niche Explorer simulation