Towards Scalable Context-Aware Single-Cell Spatial Transcriptomics Prediction from Histology Images

arXiv:2609.36429 · cs.CV · Submitted 2026-09-29 · Read on arXiv

cs.CV

Submitted: 2026-09-29

Updated: 2026-09-29

Code: https://github.com/zjgao02/CELLO

Terminology

• Spatial Transcriptomics — 29× in this paper
• Foundation Model — 17× in this paper · explained in 3 episodes
• Ablation — 10× in this paper · explained in 1 episode
• Foundation Models — 9× in this paper · explained in 7 episodes
• Accuracy — 7× in this paper · explained in 1 episode
• Benchmark — 7× in this paper · explained in 2 episodes
• Generalization — 6× in this paper · explained in 13 episodes
• Embeddings — 5× in this paper · explained in 2 episodes
• Adaptation — 4× in this paper · explained in 1 episode
• Alignment — 4× in this paper · explained in 1 episode
• Robustness — 4× in this paper · explained in 5 episodes
• Transformer — 4× in this paper · explained in 2 episodes
• Feature Extraction — 3× in this paper · explained in 2 episodes
• Ablation Studies — 2× in this paper · explained in 1 episode
• Ablation study — 2× in this paper · explained in 1 episode
• Adam — 2× in this paper · explained in 2 episodes
• Contrastive Learning — 2× in this paper · explained in 5 episodes
• External Validation — 2× in this paper · explained in 2 episodes
• Flow Matching — 2× in this paper · explained in 7 episodes
• Generative Modeling — 2× in this paper · explained in 3 episodes
• Attention Mechanism — 1× in this paper · explained in 2 episodes
• Computational Biology — 1× in this paper · explained in 2 episodes
• Data Augmentation — 1× in this paper · explained in 7 episodes
• Data Fusion — 1× in this paper · explained in 3 episodes
• Downstream Tasks — 1× in this paper · explained in 2 episodes
• Fine-Tuning — 1× in this paper · explained in 5 episodes
• Optimal Transport — 1× in this paper · explained in 5 episodes
• Segmentation Masks — 1× in this paper · explained in 2 episodes
• Self-Supervised Learning — 1× in this paper · explained in 7 episodes
• Sparsity — 1× in this paper · explained in 4 episodes
• Structural Integrity — 1× in this paper · explained in 3 episodes
• Transfer Learning — 1× in this paper · explained in 10 episodes

Sources

• Diffusion Generative Modeling for Spatially Resolved Gene Expression Inference from Histology Images
• M2ORT: Many-To-One Regression Transformer for Spatial Transcriptomics Prediction from Histopathology Images
• Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching
• DINO: DETR with Improved DeNoising Anchor Boxes for End-to-End Object Detection
• Virchow2: Scaling Self-Supervised Mixed Magnification Models in Pathology
• SToFM: a Multi-scale Foundation Model for Spatial Transcriptomics

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