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June 13, 2026National Science ReviewOpen Access

A User’s Roadmap to Foundation Models on Single-Cell and Spatial-Omics – Cell Type and Lineage applications

Qixing Yang Y Zhou Hailong Zhang Mingyu Cai Jie Hong K Li X C Xie Chengshuang Chu Chunman Zuo

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Key Points

This work aims to guide users in effectively applying foundation models to single-cell and spatial-omics data.
Developed a roadmap for utilizing foundation models in single-cell and spatial-omics contexts.
Discussed various applications, including cell type identification and lineage tracing.
Emphasized integration of bioinformatics tools for data analysis.
Identified key strategies for applying foundation models in understanding cellular heterogeneity.
Highlighted successful case studies demonstrating enhanced insights in lineage tracing.
Provided actionable insights for researchers to leverage these models in their work.

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Implication

Roadmap highlights cell type and lineage applications of foundation models in single-cell analysis, suggesting new insights.

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Cite This Study

Yang et al. (2026) studied this question.

synapsesocial.com/papers/6a323915d50b63ecad204b25 https://doi.org/10.1093/nsr/nwag371

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Synapse has enriched 5 closely related papers on similar clinical questions. Consider them for comparative context:

1Abstract 5491: AI foundation model for single cell annotation from conventional histopathology images of cancer.Original Research · 2026
2Abstract 3523: Self-supervised foundation model captures high-dimensional morphology data from single cell brightfield images2024
3Evaluating the Utilities of Foundation Models in Single‐Cell Data AnalysisOriginal Research · 2026 · 61 citations
4Abstract P24: Multi-Scale Modeling for Prediction of Spatial Single-Cell and Bulk Transcriptomic Profiles from Whole-Slide Images of Colorectal Cancer2025
5CELLama: Foundation Model for Single Cell and Spatial Transcriptomics by Cell Embedding Leveraging Language Model Abilities2025

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Abstract LB159: A practical guideline for benchmarking unimodal and multimodal foundation models on spatial transcriptomics data in oncology2026
Large Scale Foundation Model on Single-cell Transcriptomics2023
CELLama: Foundation Model for Single Cell and Spatial Transcriptomics by Cell Embedding Leveraging Language Model Abilities2024

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