SheafStain: Sheaf-Theoretic Schr\"odinger Bridge for Spatially and Biologically Coherent Virtual Staining

arXiv:2606.11846v2 Announce Type: replace Abstract: Current virtual staining approaches offer the potential for time- and cost-efficient biomarker quantification in cancer diagnostics and prognostics. However, patch-wise inference for gigapixel whole-slide images (WSIs) fails to maintain spatial continuity, yielding artifacts that cause catastrophic mismatches with ground-truth images. Although pathology Vision Foundation Models (VFMs) offer rich representations, their self-attention causes varying global contexts to produce inconsistent embeddings for the same physical region. We formalize and validate this ``context contamination'' as a sheaf-theoretic problem where these embeddings form a presheaf whose sections disagree on overlaps, so no global section restricts to them. To address this, we propose SheafStain, a new approach that reinterprets VFM features as sheaf-like sections for spatially and biologically coherent virtual staining. Specifically, SheafStain integrates class and patch tokens into a Schr\"odinger Bridge framework as sheaf-like sections. While the class token anchors biological consistency, patch tokens form a per-position spatial map. An encoder co-pretrained on Hematoxylin \& Eosin (H\&E) and Immunohistochemistry (IHC) yields cross-stain sections, so a single VFM feature space supervises both input conditioning and output stain alignment. Departing from prior work that evaluates on isolated $256 \times 256$ patches and either random-crops or resizes the $1024 \times 1024$ ground truth, we translate at $256 \times 256$ and evaluate on the stitched $1024 \times 1024$ outputs across HER2, ER, PR, and Ki-67. SheafStain demonstrates promising results against six prior methods while mitigating patch-boundary stitching artifacts. Code is available at https://github.com/deepnoid-ai/SheafStain.