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Eswar1885/tcga-luad-provgigapath-embeddings

TCGA-LUAD — Prov-GigaPath Tile Embeddings Pre-extracted 1536-dimensional tile embeddings for TCGA-LUAD diagnostic H&E whole-slide images, produced with the Prov-GigaPath tile encoder (prov-gigapath/prov-gigapath). Part of a four-encoder benchmark in which every model was run on the identical tiles for a fair comparison. Tiling (identical across all encoders in the study) Source: raw TCGA-LUAD .svs (GDC, open-access diagnostic slides). 20× / 0.5 microns per pixel… See the full description on the dataset page: https://huggingface.co/datasets/Eswar1885/tcga-luad-provgigapath-embeddings.

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TCGA-LUAD — Prov-GigaPath Tile Embeddings

Pre-extracted 1536-dimensional tile embeddings for TCGA-LUAD diagnostic H&E whole-slide images, produced with the Prov-GigaPath tile encoder (prov-gigapath/prov-gigapath). Part of a four-encoder benchmark in which every model was run on the identical tiles for a fair comparison.

Tiling (identical across all encoders in the study)

  • —Source: raw TCGA-LUAD .svs (GDC, open-access diagnostic slides).
  • —20× / 0.5 microns per pixel, MPP-aware (handles mixed 20×/40× scans).
  • —256 × 256 px tiles, non-overlapping, full tissue coverage (Otsu on HSV saturation).
  • —Prov-GigaPath's official transform (Resize 256 → CenterCrop 224 → ImageNet norm) applied per tile.

Format (per slide, CLAM-compatible)

<slide_id>.h5:

  • —features — (N, 1536) float32
  • —coords — (N, 2) int32, level-0 (x, y) of each tile
  • —attrs: patch_size=256, patch_level=0, target_mpp=0.5, model, embed_dim

slide_id = TCGA barcode + GDC file UUID. Task labels (PDS / TP53 / EGFR / KRAS) are in labels/ (schema: case_id, slide_id, label).

Cohort

531 slides / 478 patients (diagnostic FFPE, primary tumor).

Attribution & license

  • —Source model: Prov-GigaPath — Xu et al., A whole-slide foundation model for digital pathology from real-world data, Nature 2024. Model under Apache-2.0.
  • —These derived embeddings are released under CC-BY-NC 4.0, honoring the model's research-only / non-clinical intent. Not for clinical use.
  • —Source images: TCGA-LUAD (NIH/GDC), open-access.

Provided for non-commercial academic research. Please cite the Prov-GigaPath paper and TCGA when using these features.