{
  "config": {
    "amp": true,
    "batch_size": 64,
    "contour_coordinate_space": "xenium_pixel",
    "contour_geojson": "/data/taobo.hu/pyxenium_lazyslide_breast_wta_20260507/data/xenium_explorer_annotations.s1_s5.generated.geojson",
    "contour_id_key": "name",
    "contour_key": "histoseg_structures",
    "contour_pixel_size_um": null,
    "device": "cuda",
    "he_image_key": "he",
    "he_source_path": "/data/taobo.hu/pyxenium_lazyslide_breast_wta_20260507/data/WTA_Preview_FFPE_Breast_Cancer_he_image.tiffslide_pyramid.tif",
    "include_boundary_programs": true,
    "include_rna": true,
    "max_tiles": null,
    "model": "plip",
    "mpp": 0.5,
    "output_dir": "/data/taobo.hu/pyxenium_lazyslide_breast_wta_20260507/runs/direct_lazyslide_plip_full_text",
    "program_library": "tumor_boundary_v1",
    "rna_markers": [
      "EPCAM",
      "KRT8",
      "KRT18",
      "KRT19",
      "ERBB2",
      "ESR1",
      "PGR",
      "MKI67",
      "COL1A1",
      "COL1A2",
      "COL3A1",
      "DCN",
      "LUM",
      "ACTA2",
      "FAP",
      "PECAM1",
      "VWF",
      "RGS5",
      "CD3D",
      "CD3E",
      "TRAC",
      "MS4A1",
      "CD79A",
      "CXCL13",
      "CD68",
      "CD163",
      "LST1",
      "SPP1",
      "CA9",
      "SLC2A1"
    ],
    "slide_mpp": null,
    "table_format": "parquet",
    "text_terms": [
      "ductal epithelium",
      "invasive carcinoma",
      "in situ carcinoma",
      "fibrotic stroma",
      "immune infiltrate",
      "necrosis",
      "adipose tissue",
      "vascular stroma",
      "lumen or secretion"
    ],
    "tile_px": 224,
    "wsi_reader": "tiffslide"
  },
  "created_at_unix": 1778250662.4287217,
  "files": {
    "image_contours": "image_contours.parquet",
    "program_image_associations": "program_image_associations.parquet",
    "rna_image_associations": "rna_image_associations.parquet",
    "structure_differential_features": "structure_differential_features.parquet",
    "structure_image_features": "structure_image_features.parquet",
    "structure_program_scores": "structure_program_scores.parquet",
    "structure_rna_summary": "structure_rna_summary.parquet",
    "tile_assignments": "tile_assignments.parquet",
    "tile_features": "tile_features.parquet"
  },
  "git_commit": null,
  "gpu": {
    "available": true,
    "devices": [
      "NVIDIA A100-SXM4-40GB, 40960 MiB",
      "NVIDIA A100-SXM4-40GB, 40960 MiB",
      "NVIDIA A100-SXM4-40GB, 40960 MiB",
      "NVIDIA A100-SXM4-40GB, 40960 MiB",
      "NVIDIA A100-SXM4-40GB, 40960 MiB",
      "NVIDIA A100-SXM4-40GB, 40960 MiB",
      "NVIDIA A100-SXM4-40GB, 40960 MiB",
      "NVIDIA A100-SXM4-40GB, 40960 MiB"
    ]
  },
  "inputs": {
    "contour_key": "histoseg_structures",
    "he_image_key": "he",
    "he_source_path": "Y:\\long\\10X_datasets\\Xenium\\Atera\\WTA_Preview_FFPE_Breast_Cancer_outs\\WTA_Preview_FFPE_Breast_Cancer_he_image.ome.tif",
    "n_cells": 170057,
    "n_features": 18028,
    "slide_mpp": null,
    "wsi_reader": "tiffslide",
    "wsi_registry": {}
  },
  "kind": "histoseg_lazyslide_structure_workflow",
  "model_status": {
    "backend": "lazyslide",
    "lazy_module": "0.10.1",
    "model": "plip",
    "n_tiles": 3115,
    "path": "/data/taobo.hu/pyxenium_lazyslide_breast_wta_20260507/data/WTA_Preview_FFPE_Breast_Cancer_he_image.tiffslide_pyramid.tif",
    "status": "completed",
    "wsi_source": "external_override"
  },
  "outputs": {
    "assignment_fraction": 0.9996789727126806,
    "n_assigned_tiles": 3114,
    "n_contours": 1578,
    "n_tiles": 3115
  },
  "package_boundaries": {
    "HistoSeg": "Owns tissue structure segmentation and contour generation.",
    "LazySlide": "Owns WSI tiling and PLIP/CONCH image model inference.",
    "pyXenium": "Owns Xenium alignment, structure-level RNA/image summaries, and interpretable multimodal associations."
  },
  "program_status": {
    "status": "computed"
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  "runtime_seconds": 3989.328332424164,
  "sample_id": "Y:\\long\\10X_datasets\\Xenium\\Atera\\WTA_Preview_FFPE_Breast_Cancer_outs",
  "schema_version": "pyxenium-histoseg-lazyslide-v1"
}