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  1. README.md +93 -3
  2. data/TCGA-CESC/conch_v15/10x/part-00000.parquet +3 -0
  3. data/TCGA-CESC/conch_v15/20x/part-00000.parquet +3 -0
  4. data/TCGA-CESC/conch_v15/20x/part-00001.parquet +3 -0
  5. data/TCGA-CESC/conch_v15/20x/part-00002.parquet +3 -0
  6. data/TCGA-CESC/conch_v15/5x/part-00000.parquet +3 -0
  7. data/TCGA-COAD/conch_v15/10x/part-00000.parquet +3 -0
  8. data/TCGA-COAD/conch_v15/20x/part-00000.parquet +3 -0
  9. data/TCGA-COAD/conch_v15/20x/part-00001.parquet +3 -0
  10. data/TCGA-COAD/conch_v15/20x/part-00002.parquet +3 -0
  11. data/TCGA-COAD/conch_v15/20x/part-00003.parquet +3 -0
  12. data/TCGA-COAD/conch_v15/5x/part-00000.parquet +3 -0
  13. data/TCGA-KIRC/conch_v15/10x/part-00000.parquet +3 -0
  14. data/TCGA-KIRC/conch_v15/10x/part-00001.parquet +3 -0
  15. data/TCGA-KIRC/conch_v15/20x/part-00001.parquet +3 -0
  16. data/TCGA-KIRC/conch_v15/20x/part-00002.parquet +3 -0
  17. data/TCGA-KIRC/conch_v15/20x/part-00004.parquet +3 -0
  18. data/TCGA-KIRC/conch_v15/20x/part-00005.parquet +3 -0
  19. data/TCGA-KIRC/conch_v15/5x/part-00000.parquet +3 -0
  20. data/TCGA-OV/conch_v15/10x/part-00000.parquet +3 -0
  21. data/TCGA-OV/conch_v15/20x/part-00000.parquet +3 -0
  22. data/TCGA-OV/conch_v15/20x/part-00001.parquet +3 -0
  23. data/TCGA-OV/conch_v15/5x/part-00000.parquet +3 -0
  24. data/TCGA-PRAD/conch_v15/10x/part-00000.parquet +3 -0
  25. data/TCGA-PRAD/conch_v15/10x/part-00001.parquet +3 -0
  26. data/TCGA-PRAD/conch_v15/20x/part-00000.parquet +3 -0
  27. data/TCGA-PRAD/conch_v15/20x/part-00001.parquet +3 -0
  28. data/TCGA-PRAD/conch_v15/20x/part-00002.parquet +3 -0
  29. data/TCGA-PRAD/conch_v15/20x/part-00003.parquet +3 -0
  30. data/TCGA-PRAD/conch_v15/20x/part-00004.parquet +3 -0
  31. data/TCGA-PRAD/conch_v15/5x/part-00000.parquet +3 -0
  32. data/TCGA-READ/conch_v15/10x/part-00000.parquet +3 -0
  33. data/TCGA-READ/conch_v15/20x/part-00000.parquet +3 -0
  34. data/TCGA-READ/conch_v15/5x/part-00000.parquet +3 -0
  35. data/TCGA-UCEC/conch_v15/10x/part-00000.parquet +3 -0
  36. data/TCGA-UCEC/conch_v15/10x/part-00001.parquet +3 -0
  37. data/TCGA-UCEC/conch_v15/20x/part-00000.parquet +3 -0
  38. data/TCGA-UCEC/conch_v15/20x/part-00001.parquet +3 -0
  39. data/TCGA-UCEC/conch_v15/20x/part-00002.parquet +3 -0
  40. data/TCGA-UCEC/conch_v15/20x/part-00003.parquet +3 -0
  41. data/TCGA-UCEC/conch_v15/20x/part-00004.parquet +3 -0
  42. data/TCGA-UCEC/conch_v15/20x/part-00005.parquet +3 -0
  43. data/TCGA-UCEC/conch_v15/20x/part-00006.parquet +3 -0
  44. data/TCGA-UCEC/conch_v15/20x/part-00007.parquet +3 -0
  45. data/TCGA-UCEC/conch_v15/5x/part-00000.parquet +3 -0
  46. data/TCGA-UVM/conch_v15/10x/part-00000.parquet +3 -0
  47. data/TCGA-UVM/conch_v15/5x/part-00000.parquet +3 -0
  48. metadata/nested_index.json +333 -0
  49. metadata/shard_manifest.parquet +3 -0
  50. metadata/slide_registry.parquet +3 -0
README.md CHANGED
@@ -1,5 +1,95 @@
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  ---
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- license: other
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- license_name: copyleft
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- license_link: LICENSE
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
5
  ---
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
  ---
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+ configs:
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+ - config_name: conch_v15_20x
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+ data_files:
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+ - split: TCGA_ACC
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+ path: data/TCGA-ACC/conch_v15/20x/*.parquet
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+ - split: TCGA_BLCA
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+ path: data/TCGA-BLCA/conch_v15/20x/*.parquet
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+ - split: TCGA_BRCA
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+ path: data/TCGA-BRCA/conch_v15/20x/*.parquet
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+ - split: TCGA_CESC
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+ path: data/TCGA-CESC/conch_v15/20x/*.parquet
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+ - split: TCGA_CHOL
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+ path: data/TCGA-CHOL/conch_v15/20x/*.parquet
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+ - split: TCGA_COAD
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+ path: data/TCGA-COAD/conch_v15/20x/*.parquet
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+ - split: TCGA_DLBC
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+ path: data/TCGA-DLBC/conch_v15/20x/*.parquet
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+ - split: TCGA_ESCA
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+ path: data/TCGA-ESCA/conch_v15/20x/*.parquet
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+ - split: TCGA_GBM
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+ path: data/TCGA-GBM/conch_v15/20x/*.parquet
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+ - split: TCGA_HNSC
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+ path: data/TCGA-HNSC/conch_v15/20x/*.parquet
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+ - split: TCGA_KICH
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+ path: data/TCGA-KICH/conch_v15/20x/*.parquet
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+ - split: TCGA_KIRC
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+ path: data/TCGA-KIRC/conch_v15/20x/*.parquet
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+ - split: TCGA_KIRP
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+ path: data/TCGA-KIRP/conch_v15/20x/*.parquet
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+ - split: TCGA_LGG
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+ path: data/TCGA-LGG/conch_v15/20x/*.parquet
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+ - split: TCGA_LIHC
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+ path: data/TCGA-LIHC/conch_v15/20x/*.parquet
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+ - split: TCGA_LUAD
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+ path: data/TCGA-LUAD/conch_v15/20x/*.parquet
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+ - split: TCGA_LUSC
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+ path: data/TCGA-LUSC/conch_v15/20x/*.parquet
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+ - split: TCGA_MESO
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+ path: data/TCGA-MESO/conch_v15/20x/*.parquet
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+ - split: TCGA_OV
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+ path: data/TCGA-OV/conch_v15/20x/*.parquet
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+ - split: TCGA_PAAD
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+ path: data/TCGA-PAAD/conch_v15/20x/*.parquet
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+ - split: TCGA_PCPG
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+ path: data/TCGA-PCPG/conch_v15/20x/*.parquet
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+ - split: TCGA_PRAD
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+ path: data/TCGA-PRAD/conch_v15/20x/*.parquet
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+ - split: TCGA_READ
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+ path: data/TCGA-READ/conch_v15/20x/*.parquet
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+ - split: TCGA_SARC
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+ path: data/TCGA-SARC/conch_v15/20x/*.parquet
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+ - split: TCGA_SKCM
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+ path: data/TCGA-SKCM/conch_v15/20x/*.parquet
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+ - split: TCGA_STAD
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+ path: data/TCGA-STAD/conch_v15/20x/*.parquet
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+ - split: TCGA_TGCT
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+ path: data/TCGA-TGCT/conch_v15/20x/*.parquet
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+ - split: TCGA_THCA
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+ path: data/TCGA-THCA/conch_v15/20x/*.parquet
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+ - split: TCGA_THYM
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+ path: data/TCGA-THYM/conch_v15/20x/*.parquet
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+ - split: TCGA_UCEC
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+ path: data/TCGA-UCEC/conch_v15/20x/*.parquet
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+ - split: TCGA_UCS
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+ path: data/TCGA-UCS/conch_v15/20x/*.parquet
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+ - split: TCGA_UVM
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+ path: data/TCGA-UVM/conch_v15/20x/*.parquet
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  ---
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+
71
+ # TCGA Pathology Feature Atlas
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+
73
+ This repository stores pathology foundation-model embeddings as sharded Parquet files.
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+
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+ Physical layout:
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+
77
+ ```text
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+ data/{project_id}/{model_name}/{magnification}/part-*.parquet
79
+ ```
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+
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+ Example:
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+
83
+ ```text
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+ data/TCGA-BRCA/conch_v15/20x/part-00000.parquet
85
+ ```
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+
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+ Example streaming load:
88
+
89
+ ```python
90
+ from datasets import load_dataset
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+
92
+ ds = load_dataset("IUCompPath/CRAFT", name="conch_v15_20x", split="TCGA_BRCA", streaming=True)
93
+ ```
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+
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+ Each row is a chunk of patch embeddings from one slide.
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