H&E → spatial transcriptomics prediction (HE-zoo)

Predict spot-level (or sub-spot-level) gene expression directly from H&E histology images. Every notebook below predicts on the same 10x Visium Breast Cancer Block A Section 1 H&E so the four backends are directly comparable; HEST-FM / STPath / STFlow additionally re-run on Section 2 of the same patient block as a held-out “never-seen H&E” check.

See Tutorials-space/he-zoo/index.md for the per-backend feature matrix and “which to pick when” guidance.

• HEST-FM — pathology foundation model + ridge head
• STPath — zero-shot generative foundation model
• STFlow — per-slide flow-matching denoiser
• iStar — super-resolve a paired Visium + H&E sample