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TRACE

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  1. README.md +13 -89
  2. data/TCGA-ACC/gigapath_slide/20x/part-00000.parquet +3 -0
  3. data/TCGA-ACC/titan/20x/part-00000.parquet +3 -0
  4. data/TCGA-BLCA/gigapath_slide/20x/part-00000.parquet +3 -0
  5. data/TCGA-BLCA/titan/20x/part-00000.parquet +3 -0
  6. data/TCGA-CESC/gigapath_slide/20x/part-00000.parquet +3 -0
  7. data/TCGA-CESC/titan/20x/part-00000.parquet +3 -0
  8. data/TCGA-COAD/gigapath_slide/20x/part-00000.parquet +3 -0
  9. data/TCGA-COAD/titan/20x/part-00000.parquet +3 -0
  10. data/TCGA-ESCA/gigapath_slide/20x/part-00000.parquet +3 -0
  11. data/TCGA-GBM/gigapath_slide/20x/part-00000.parquet +3 -0
  12. data/TCGA-GBM/titan/20x/part-00000.parquet +3 -0
  13. data/TCGA-HNSC/gigapath_slide/20x/part-00000.parquet +3 -0
  14. data/TCGA-HNSC/titan/20x/part-00000.parquet +3 -0
  15. data/TCGA-KICH/gigapath_slide/20x/part-00000.parquet +3 -0
  16. data/TCGA-KIRC/gigapath_slide/20x/part-00000.parquet +3 -0
  17. data/TCGA-KIRC/titan/20x/part-00000.parquet +3 -0
  18. data/TCGA-KIRP/gigapath_slide/20x/part-00000.parquet +3 -0
  19. data/TCGA-KIRP/titan/20x/part-00000.parquet +3 -0
  20. data/TCGA-LGG/gigapath_slide/20x/part-00000.parquet +3 -0
  21. data/TCGA-LGG/titan/20x/part-00000.parquet +3 -0
  22. data/TCGA-LUAD/gigapath_slide/20x/part-00000.parquet +3 -0
  23. data/TCGA-LUAD/titan/20x/part-00000.parquet +3 -0
  24. data/TCGA-MESO/gigapath_slide/20x/part-00000.parquet +3 -0
  25. data/TCGA-MESO/titan/20x/part-00000.parquet +3 -0
  26. data/TCGA-OV/gigapath_slide/20x/part-00000.parquet +3 -0
  27. data/TCGA-OV/titan/20x/part-00000.parquet +3 -0
  28. data/TCGA-PAAD/gigapath_slide/20x/part-00000.parquet +3 -0
  29. data/TCGA-PRAD/gigapath_slide/20x/part-00000.parquet +3 -0
  30. data/TCGA-PRAD/titan/20x/part-00000.parquet +3 -0
  31. data/TCGA-READ/gigapath_slide/20x/part-00000.parquet +3 -0
  32. data/TCGA-READ/titan/20x/part-00000.parquet +3 -0
  33. data/TCGA-SARC/gigapath_slide/20x/part-00000.parquet +3 -0
  34. data/TCGA-SKCM/titan/20x/part-00000.parquet +3 -0
  35. data/TCGA-TGCT/gigapath_slide/20x/part-00000.parquet +3 -0
  36. data/TCGA-TGCT/titan/20x/part-00000.parquet +3 -0
  37. data/TCGA-THCA/gigapath_slide/20x/part-00000.parquet +3 -0
  38. data/TCGA-THCA/titan/20x/part-00000.parquet +3 -0
  39. data/TCGA-THYM/gigapath_slide/20x/part-00000.parquet +3 -0
  40. data/TCGA-THYM/titan/20x/part-00000.parquet +3 -0
  41. data/TCGA-UCEC/gigapath_slide/20x/part-00000.parquet +3 -0
  42. data/TCGA-UCEC/titan/20x/part-00000.parquet +3 -0
  43. data/TCGA-UVM/gigapath_slide/20x/part-00000.parquet +3 -0
  44. data/TCGA-UVM/titan/20x/part-00000.parquet +3 -0
  45. metadata/h5_validation.parquet +3 -0
  46. metadata/nested_index.json +386 -0
  47. metadata/release.json +78 -0
  48. metadata/shard_manifest.parquet +3 -0
  49. metadata/slide_registry.parquet +3 -0
  50. metadata/upload_status.json +2179 -0
README.md CHANGED
@@ -1,95 +1,19 @@
1
- ---
2
- configs:
3
- - config_name: conch_v15_10x
4
- data_files:
5
- - split: TCGA_ACC
6
- path: data/TCGA-ACC/conch_v15/10x/*.parquet
7
- - split: TCGA_BLCA
8
- path: data/TCGA-BLCA/conch_v15/10x/*.parquet
9
- - split: TCGA_BRCA
10
- path: data/TCGA-BRCA/conch_v15/10x/*.parquet
11
- - split: TCGA_CESC
12
- path: data/TCGA-CESC/conch_v15/10x/*.parquet
13
- - split: TCGA_CHOL
14
- path: data/TCGA-CHOL/conch_v15/10x/*.parquet
15
- - split: TCGA_COAD
16
- path: data/TCGA-COAD/conch_v15/10x/*.parquet
17
- - split: TCGA_DLBC
18
- path: data/TCGA-DLBC/conch_v15/10x/*.parquet
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- - split: TCGA_ESCA
20
- path: data/TCGA-ESCA/conch_v15/10x/*.parquet
21
- - split: TCGA_GBM
22
- path: data/TCGA-GBM/conch_v15/10x/*.parquet
23
- - split: TCGA_HNSC
24
- path: data/TCGA-HNSC/conch_v15/10x/*.parquet
25
- - split: TCGA_KICH
26
- path: data/TCGA-KICH/conch_v15/10x/*.parquet
27
- - split: TCGA_KIRC
28
- path: data/TCGA-KIRC/conch_v15/10x/*.parquet
29
- - split: TCGA_KIRP
30
- path: data/TCGA-KIRP/conch_v15/10x/*.parquet
31
- - split: TCGA_LGG
32
- path: data/TCGA-LGG/conch_v15/10x/*.parquet
33
- - split: TCGA_LIHC
34
- path: data/TCGA-LIHC/conch_v15/10x/*.parquet
35
- - split: TCGA_LUAD
36
- path: data/TCGA-LUAD/conch_v15/10x/*.parquet
37
- - split: TCGA_LUSC
38
- path: data/TCGA-LUSC/conch_v15/10x/*.parquet
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- - split: TCGA_MESO
40
- path: data/TCGA-MESO/conch_v15/10x/*.parquet
41
- - split: TCGA_OV
42
- path: data/TCGA-OV/conch_v15/10x/*.parquet
43
- - split: TCGA_PAAD
44
- path: data/TCGA-PAAD/conch_v15/10x/*.parquet
45
- - split: TCGA_PCPG
46
- path: data/TCGA-PCPG/conch_v15/10x/*.parquet
47
- - split: TCGA_PRAD
48
- path: data/TCGA-PRAD/conch_v15/10x/*.parquet
49
- - split: TCGA_READ
50
- path: data/TCGA-READ/conch_v15/10x/*.parquet
51
- - split: TCGA_SARC
52
- path: data/TCGA-SARC/conch_v15/10x/*.parquet
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- - split: TCGA_SKCM
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- path: data/TCGA-SKCM/conch_v15/10x/*.parquet
55
- - split: TCGA_STAD
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- path: data/TCGA-STAD/conch_v15/10x/*.parquet
57
- - split: TCGA_TGCT
58
- path: data/TCGA-TGCT/conch_v15/10x/*.parquet
59
- - split: TCGA_THCA
60
- path: data/TCGA-THCA/conch_v15/10x/*.parquet
61
- - split: TCGA_THYM
62
- path: data/TCGA-THYM/conch_v15/10x/*.parquet
63
- - split: TCGA_UCEC
64
- path: data/TCGA-UCEC/conch_v15/10x/*.parquet
65
- - split: TCGA_UCS
66
- path: data/TCGA-UCS/conch_v15/10x/*.parquet
67
- - split: TCGA_UVM
68
- path: data/TCGA-UVM/conch_v15/10x/*.parquet
69
- ---
70
 
71
- # TCGA Pathology Feature Atlas
72
 
73
- This repository stores pathology foundation-model embeddings as sharded Parquet files.
74
 
75
- Physical layout:
 
76
 
77
- ```text
78
- data/{project_id}/{model_name}/{magnification}/part-*.parquet
79
- ```
80
 
81
- Example:
 
 
 
 
82
 
83
- ```text
84
- data/TCGA-BRCA/conch_v15/20x/part-00000.parquet
85
- ```
86
-
87
- Example streaming load:
88
-
89
- ```python
90
- from datasets import load_dataset
91
-
92
- ds = load_dataset("IUCompPath/CRAFT", name="conch_v15_20x", split="TCGA_BRCA", streaming=True)
93
- ```
94
-
95
- Each row is a chunk of patch embeddings from one slide.
 
1
+ # TCGA Pathology Atlas — partial release
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
2
 
3
+ This is a staged partial release for `IUCompPath/TRACE`.
4
 
5
+ ## Included models
6
 
7
+ - `gigapath_slide`
8
+ - `titan`
9
 
10
+ ## Scope
 
 
11
 
12
+ - Groups: 64
13
+ - Shards: 64
14
+ - Embedding rows: 23,336
15
+ - Compressed Parquet bytes: 152,218,294
16
+ - H5 validation failures: 0
17
 
18
+ This release intentionally excludes `midnight12k` and unavailable or quarantined source groups.
19
+ See `metadata/upload_status.json` for the model × project × magnification upload ledger.
 
 
 
 
 
 
 
 
 
 
 
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