[
  {
    "structure_id": 1,
    "pre_visual_name": "S1 invasive ductal carcinoma [S1]",
    "final_name": "invasive ductal carcinoma [S1]",
    "visual_override": false,
    "accepted": false,
    "confidence": 0.89,
    "foundation_top_label": "Artifact or low-quality tissue",
    "foundation_top_score": 0.8685594797134399,
    "reasoning_summary": "The H&E foundation model flags a large proportion of the region as \"Artifact or low-quality tissue\" (82 contours, max score 0.87) and also identifies macrophage‑rich inflammation, ductal carcinoma in situ/ductal tumor, and invasive tumor epithelium. While the artifact label dominates, the presence of invasive tumor epithelium (57 contours) and DCIS‑like patterns (54 contours) indicates genuine neoplastic tissue amidst inflammation and some tissue degradation. Molecular evidence from the Xenium WTA data strongly supports an invasive breast carcinoma diagnosis: the top multimodal candidate is \"invasive ductal carcinoma\" with a total score of 0.805, anchored by neoplastic luminal epithelial cells (14.1%) and secretory luminal tumor cells (7.2%). The composition is dominated by lymphocytes (≈64%) and a measurable invasive carcinoma cell fraction (5.3%). Because the molecular signature is consistent with IDC and the visual tumor signals, the visual evidence does not outweigh the molecular diagnosis, so no visual override is applied.",
    "error": null
  },
  {
    "structure_id": 2,
    "pre_visual_name": "S2 reactive breast stroma [S2]",
    "final_name": "reactive breast stroma",
    "visual_override": false,
    "accepted": false,
    "confidence": 0.96,
    "foundation_top_label": "Macrophage-rich inflammation",
    "foundation_top_score": 0.9507338404655457,
    "reasoning_summary": "The H&E foundation model assigns the region a top visual label of \"Macrophage‑rich inflammation\" with a high foundation score (0.95). However, the molecular (10x Xenium) evidence shows a composition dominated by fibroblasts (≈40%), endothelial cells (≈27%) and myofibroblasts (≈15%), with only ~3% macrophages. The multimodal candidate ranking places \"reactive breast stroma\" far above all other options (total score 5.61 vs 3.31 for vascular stroma). The cell‑type profile and the high anchor‑coverage (1.0) strongly support a stromal, non‑neoplastic interpretation. Because the H&E label conflicts with the molecular profile and the latter is biologically more plausible, no visual override is applied.",
    "error": null
  },
  {
    "structure_id": 3,
    "pre_visual_name": "S3 invasive ductal carcinoma [S3]",
    "final_name": "S3 invasive ductal carcinoma [S3]",
    "visual_override": false,
    "accepted": false,
    "confidence": 0.876,
    "foundation_top_label": "Macrophage-rich inflammation",
    "foundation_top_score": 0.9596852660179138,
    "reasoning_summary": "The multimodal molecular evidence (harmonized composition: 54.5% neoplastic luminal epithelial, 13.6% invasive carcinoma cells, 22.7% luminal epithelial, 9.1% myoepithelial) and the top candidate score (0.6826) robustly support an invasive ductal carcinoma of no special type. The H&E foundation model flags a dominant \"Macrophage‑rich inflammation\" label (639 contours, max score 0.96), reflecting a heavy infiltrate of tumor‑associated macrophages rather than a primary inflammatory lesion. Given the overwhelming neoplastic cell composition and the behavior label (invasive) from the molecular pipeline, the visual finding is interpreted as tumor‑associated inflammation within IDC, not a contradictory diagnosis. Therefore no visual override is applied.",
    "error": null
  },
  {
    "structure_id": 4,
    "pre_visual_name": "S4 reactive breast stroma [S4]",
    "final_name": "S4 reactive breast stroma [S4]",
    "visual_override": false,
    "accepted": false,
    "confidence": 0.32,
    "foundation_top_label": "Macrophage-rich inflammation",
    "foundation_top_score": 0.9617540240287781,
    "reasoning_summary": "The H&E foundation model assigns the region primarily to \"Macrophage‑rich inflammation\" (max score 0.96) and also flags vascular, fibrocollagenous, artifact and necrosis labels. However, the multimodal molecular profile is dominated by myoepithelial cells (≈77% myoepithelial, 81% basal/myoepithelial cluster) with a smaller but notable presence of luminal tumor cells. The top multimodal candidate is \"reactive breast stroma\" with the highest total score among all candidates, despite a negative absolute score due to hard‑rule penalties. The inflammatory H&E signal likely reflects a secondary infiltrate or artifact rather than the primary tissue architecture. Because the visual evidence does not meet the override confidence threshold (LLM confidence 0.19 < 0.7) and the molecular data more plausibly explain the cellular composition, we retain the original stroma label without visual override.",
    "error": null
  }
]