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  1. README.md +34 -34
  2. metadata/nested_index.json +93 -183
  3. metadata/shard_manifest.parquet +2 -2
  4. metadata/slide_registry.parquet +1 -1
README.md CHANGED
@@ -1,71 +1,71 @@
1
  ---
2
  configs:
3
- - config_name: conch_v15_20x
4
  data_files:
5
  - split: TCGA_ACC
6
- path: data/TCGA-ACC/conch_v15/20x/*.parquet
7
  - split: TCGA_BLCA
8
- path: data/TCGA-BLCA/conch_v15/20x/*.parquet
9
  - split: TCGA_BRCA
10
- path: data/TCGA-BRCA/conch_v15/20x/*.parquet
11
  - split: TCGA_CESC
12
- path: data/TCGA-CESC/conch_v15/20x/*.parquet
13
  - split: TCGA_CHOL
14
- path: data/TCGA-CHOL/conch_v15/20x/*.parquet
15
  - split: TCGA_COAD
16
- path: data/TCGA-COAD/conch_v15/20x/*.parquet
17
  - split: TCGA_DLBC
18
- path: data/TCGA-DLBC/conch_v15/20x/*.parquet
19
  - split: TCGA_ESCA
20
- path: data/TCGA-ESCA/conch_v15/20x/*.parquet
21
  - split: TCGA_GBM
22
- path: data/TCGA-GBM/conch_v15/20x/*.parquet
23
  - split: TCGA_HNSC
24
- path: data/TCGA-HNSC/conch_v15/20x/*.parquet
25
  - split: TCGA_KICH
26
- path: data/TCGA-KICH/conch_v15/20x/*.parquet
27
  - split: TCGA_KIRC
28
- path: data/TCGA-KIRC/conch_v15/20x/*.parquet
29
  - split: TCGA_KIRP
30
- path: data/TCGA-KIRP/conch_v15/20x/*.parquet
31
  - split: TCGA_LGG
32
- path: data/TCGA-LGG/conch_v15/20x/*.parquet
33
  - split: TCGA_LIHC
34
- path: data/TCGA-LIHC/conch_v15/20x/*.parquet
35
  - split: TCGA_LUAD
36
- path: data/TCGA-LUAD/conch_v15/20x/*.parquet
37
  - split: TCGA_LUSC
38
- path: data/TCGA-LUSC/conch_v15/20x/*.parquet
39
  - split: TCGA_MESO
40
- path: data/TCGA-MESO/conch_v15/20x/*.parquet
41
  - split: TCGA_OV
42
- path: data/TCGA-OV/conch_v15/20x/*.parquet
43
  - split: TCGA_PAAD
44
- path: data/TCGA-PAAD/conch_v15/20x/*.parquet
45
  - split: TCGA_PCPG
46
- path: data/TCGA-PCPG/conch_v15/20x/*.parquet
47
  - split: TCGA_PRAD
48
- path: data/TCGA-PRAD/conch_v15/20x/*.parquet
49
  - split: TCGA_READ
50
- path: data/TCGA-READ/conch_v15/20x/*.parquet
51
  - split: TCGA_SARC
52
- path: data/TCGA-SARC/conch_v15/20x/*.parquet
53
  - split: TCGA_SKCM
54
- path: data/TCGA-SKCM/conch_v15/20x/*.parquet
55
  - split: TCGA_STAD
56
- path: data/TCGA-STAD/conch_v15/20x/*.parquet
57
  - split: TCGA_TGCT
58
- path: data/TCGA-TGCT/conch_v15/20x/*.parquet
59
  - split: TCGA_THCA
60
- path: data/TCGA-THCA/conch_v15/20x/*.parquet
61
  - split: TCGA_THYM
62
- path: data/TCGA-THYM/conch_v15/20x/*.parquet
63
  - split: TCGA_UCEC
64
- path: data/TCGA-UCEC/conch_v15/20x/*.parquet
65
  - split: TCGA_UCS
66
- path: data/TCGA-UCS/conch_v15/20x/*.parquet
67
  - split: TCGA_UVM
68
- path: data/TCGA-UVM/conch_v15/20x/*.parquet
69
  ---
70
 
71
  # TCGA Pathology Feature Atlas
@@ -89,7 +89,7 @@ Example streaming load:
89
  ```python
90
  from datasets import load_dataset
91
 
92
- ds = load_dataset("IUCompPath/TRACE", name="conch_v15_20x", split="TCGA_BRCA", streaming=True)
93
  ```
94
 
95
  Each row is a chunk of patch embeddings from one slide.
 
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
19
  - 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
39
  - 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
53
  - split: TCGA_SKCM
54
+ path: data/TCGA-SKCM/conch_v15/10x/*.parquet
55
  - split: TCGA_STAD
56
+ 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
 
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.
metadata/nested_index.json CHANGED
@@ -1,332 +1,242 @@
1
  {
2
  "TCGA-DLBC": {
3
  "conch_v15": {
4
- "20x": [
5
- "data/TCGA-DLBC/conch_v15/20x/part-00000.parquet"
6
  ]
7
  }
8
  },
9
  "TCGA-CHOL": {
10
  "conch_v15": {
11
- "20x": [
12
- "data/TCGA-CHOL/conch_v15/20x/part-00000.parquet"
13
  ]
14
  }
15
  },
16
  "TCGA-ESCA": {
17
  "conch_v15": {
18
- "20x": [
19
- "data/TCGA-ESCA/conch_v15/20x/part-00000.parquet",
20
- "data/TCGA-ESCA/conch_v15/20x/part-00001.parquet"
21
  ]
22
  }
23
  },
24
  "TCGA-CESC": {
25
  "conch_v15": {
26
- "20x": [
27
- "data/TCGA-CESC/conch_v15/20x/part-00000.parquet",
28
- "data/TCGA-CESC/conch_v15/20x/part-00001.parquet",
29
- "data/TCGA-CESC/conch_v15/20x/part-00002.parquet"
30
  ]
31
  }
32
  },
33
  "TCGA-KICH": {
34
  "conch_v15": {
35
- "20x": [
36
- "data/TCGA-KICH/conch_v15/20x/part-00000.parquet",
37
- "data/TCGA-KICH/conch_v15/20x/part-00001.parquet"
38
  ]
39
  }
40
  },
41
  "TCGA-ACC": {
42
  "conch_v15": {
43
- "20x": [
44
- "data/TCGA-ACC/conch_v15/20x/part-00000.parquet",
45
- "data/TCGA-ACC/conch_v15/20x/part-00001.parquet",
46
- "data/TCGA-ACC/conch_v15/20x/part-00002.parquet",
47
- "data/TCGA-ACC/conch_v15/20x/part-00003.parquet"
48
  ]
49
  }
50
  },
51
  "TCGA-COAD": {
52
  "conch_v15": {
53
- "20x": [
54
- "data/TCGA-COAD/conch_v15/20x/part-00000.parquet",
55
- "data/TCGA-COAD/conch_v15/20x/part-00001.parquet",
56
- "data/TCGA-COAD/conch_v15/20x/part-00002.parquet",
57
- "data/TCGA-COAD/conch_v15/20x/part-00003.parquet"
58
  ]
59
  }
60
  },
61
  "TCGA-HNSC": {
62
  "conch_v15": {
63
- "20x": [
64
- "data/TCGA-HNSC/conch_v15/20x/part-00000.parquet",
65
- "data/TCGA-HNSC/conch_v15/20x/part-00001.parquet",
66
- "data/TCGA-HNSC/conch_v15/20x/part-00002.parquet",
67
- "data/TCGA-HNSC/conch_v15/20x/part-00003.parquet",
68
- "data/TCGA-HNSC/conch_v15/20x/part-00004.parquet"
69
- ]
70
- }
71
- },
72
- "TCGA-KIRP": {
73
- "conch_v15": {
74
- "20x": [
75
- "data/TCGA-KIRP/conch_v15/20x/part-00000.parquet",
76
- "data/TCGA-KIRP/conch_v15/20x/part-00001.parquet",
77
- "data/TCGA-KIRP/conch_v15/20x/part-00002.parquet",
78
- "data/TCGA-KIRP/conch_v15/20x/part-00003.parquet"
79
  ]
80
  }
81
  },
82
  "TCGA-BLCA": {
83
  "conch_v15": {
84
- "20x": [
85
- "data/TCGA-BLCA/conch_v15/20x/part-00000.parquet",
86
- "data/TCGA-BLCA/conch_v15/20x/part-00001.parquet",
87
- "data/TCGA-BLCA/conch_v15/20x/part-00002.parquet",
88
- "data/TCGA-BLCA/conch_v15/20x/part-00003.parquet",
89
- "data/TCGA-BLCA/conch_v15/20x/part-00004.parquet",
90
- "data/TCGA-BLCA/conch_v15/20x/part-00005.parquet",
91
- "data/TCGA-BLCA/conch_v15/20x/part-00006.parquet"
92
  ]
93
  }
94
  },
95
- "TCGA-GBM": {
96
  "conch_v15": {
97
- "20x": [
98
- "data/TCGA-GBM/conch_v15/20x/part-00000.parquet",
99
- "data/TCGA-GBM/conch_v15/20x/part-00001.parquet",
100
- "data/TCGA-GBM/conch_v15/20x/part-00002.parquet",
101
- "data/TCGA-GBM/conch_v15/20x/part-00003.parquet",
102
- "data/TCGA-GBM/conch_v15/20x/part-00004.parquet",
103
- "data/TCGA-GBM/conch_v15/20x/part-00005.parquet",
104
- "data/TCGA-GBM/conch_v15/20x/part-00006.parquet"
105
  ]
106
  }
107
  },
108
  "TCGA-MESO": {
109
  "conch_v15": {
110
- "20x": [
111
- "data/TCGA-MESO/conch_v15/20x/part-00000.parquet"
112
  ]
113
  }
114
  },
115
  "TCGA-LIHC": {
116
  "conch_v15": {
117
- "20x": [
118
- "data/TCGA-LIHC/conch_v15/20x/part-00000.parquet",
119
- "data/TCGA-LIHC/conch_v15/20x/part-00001.parquet",
120
- "data/TCGA-LIHC/conch_v15/20x/part-00002.parquet",
121
- "data/TCGA-LIHC/conch_v15/20x/part-00003.parquet"
122
  ]
123
  }
124
  },
125
- "TCGA-KIRC": {
126
  "conch_v15": {
127
- "20x": [
128
- "data/TCGA-KIRC/conch_v15/20x/part-00000.parquet",
129
- "data/TCGA-KIRC/conch_v15/20x/part-00001.parquet",
130
- "data/TCGA-KIRC/conch_v15/20x/part-00002.parquet",
131
- "data/TCGA-KIRC/conch_v15/20x/part-00003.parquet",
132
- "data/TCGA-KIRC/conch_v15/20x/part-00004.parquet",
133
- "data/TCGA-KIRC/conch_v15/20x/part-00005.parquet"
134
  ]
135
  }
136
  },
137
  "TCGA-OV": {
138
  "conch_v15": {
139
- "20x": [
140
- "data/TCGA-OV/conch_v15/20x/part-00000.parquet",
141
- "data/TCGA-OV/conch_v15/20x/part-00001.parquet"
142
  ]
143
  }
144
  },
145
- "TCGA-READ": {
146
  "conch_v15": {
147
- "20x": [
148
- "data/TCGA-READ/conch_v15/20x/part-00000.parquet"
 
149
  ]
150
  }
151
  },
152
- "TCGA-LUAD": {
153
  "conch_v15": {
154
- "20x": [
155
- "data/TCGA-LUAD/conch_v15/20x/part-00000.parquet",
156
- "data/TCGA-LUAD/conch_v15/20x/part-00001.parquet",
157
- "data/TCGA-LUAD/conch_v15/20x/part-00002.parquet",
158
- "data/TCGA-LUAD/conch_v15/20x/part-00003.parquet",
159
- "data/TCGA-LUAD/conch_v15/20x/part-00004.parquet",
160
- "data/TCGA-LUAD/conch_v15/20x/part-00005.parquet"
161
  ]
162
  }
163
  },
164
  "TCGA-PAAD": {
165
  "conch_v15": {
166
- "20x": [
167
- "data/TCGA-PAAD/conch_v15/20x/part-00000.parquet",
168
- "data/TCGA-PAAD/conch_v15/20x/part-00001.parquet",
169
- "data/TCGA-PAAD/conch_v15/20x/part-00002.parquet"
 
 
 
 
 
 
170
  ]
171
  }
172
  },
173
  "TCGA-PCPG": {
174
  "conch_v15": {
175
- "20x": [
176
- "data/TCGA-PCPG/conch_v15/20x/part-00000.parquet",
177
- "data/TCGA-PCPG/conch_v15/20x/part-00001.parquet",
178
- "data/TCGA-PCPG/conch_v15/20x/part-00002.parquet"
179
  ]
180
  }
181
  },
182
  "TCGA-LGG": {
183
  "conch_v15": {
184
- "20x": [
185
- "data/TCGA-LGG/conch_v15/20x/part-00000.parquet",
186
- "data/TCGA-LGG/conch_v15/20x/part-00001.parquet",
187
- "data/TCGA-LGG/conch_v15/20x/part-00002.parquet",
188
- "data/TCGA-LGG/conch_v15/20x/part-00003.parquet",
189
- "data/TCGA-LGG/conch_v15/20x/part-00004.parquet",
190
- "data/TCGA-LGG/conch_v15/20x/part-00005.parquet",
191
- "data/TCGA-LGG/conch_v15/20x/part-00006.parquet"
192
  ]
193
  }
194
  },
195
  "TCGA-LUSC": {
196
  "conch_v15": {
197
- "20x": [
198
- "data/TCGA-LUSC/conch_v15/20x/part-00000.parquet",
199
- "data/TCGA-LUSC/conch_v15/20x/part-00001.parquet",
200
- "data/TCGA-LUSC/conch_v15/20x/part-00002.parquet",
201
- "data/TCGA-LUSC/conch_v15/20x/part-00003.parquet",
202
- "data/TCGA-LUSC/conch_v15/20x/part-00004.parquet"
203
  ]
204
  }
205
  },
206
  "TCGA-BRCA": {
207
  "conch_v15": {
208
- "20x": [
209
- "data/TCGA-BRCA/conch_v15/20x/part-00000.parquet",
210
- "data/TCGA-BRCA/conch_v15/20x/part-00001.parquet",
211
- "data/TCGA-BRCA/conch_v15/20x/part-00002.parquet",
212
- "data/TCGA-BRCA/conch_v15/20x/part-00003.parquet",
213
- "data/TCGA-BRCA/conch_v15/20x/part-00004.parquet",
214
- "data/TCGA-BRCA/conch_v15/20x/part-00005.parquet",
215
- "data/TCGA-BRCA/conch_v15/20x/part-00006.parquet",
216
- "data/TCGA-BRCA/conch_v15/20x/part-00007.parquet",
217
- "data/TCGA-BRCA/conch_v15/20x/part-00008.parquet",
218
- "data/TCGA-BRCA/conch_v15/20x/part-00009.parquet",
219
- "data/TCGA-BRCA/conch_v15/20x/part-00010.parquet",
220
- "data/TCGA-BRCA/conch_v15/20x/part-00011.parquet",
221
- "data/TCGA-BRCA/conch_v15/20x/part-00012.parquet"
222
  ]
223
  }
224
  },
225
  "TCGA-PRAD": {
226
  "conch_v15": {
227
- "20x": [
228
- "data/TCGA-PRAD/conch_v15/20x/part-00000.parquet",
229
- "data/TCGA-PRAD/conch_v15/20x/part-00001.parquet",
230
- "data/TCGA-PRAD/conch_v15/20x/part-00002.parquet",
231
- "data/TCGA-PRAD/conch_v15/20x/part-00003.parquet",
232
- "data/TCGA-PRAD/conch_v15/20x/part-00004.parquet"
233
  ]
234
  }
235
  },
236
  "TCGA-TGCT": {
237
  "conch_v15": {
238
- "20x": [
239
- "data/TCGA-TGCT/conch_v15/20x/part-00000.parquet",
240
- "data/TCGA-TGCT/conch_v15/20x/part-00001.parquet",
241
- "data/TCGA-TGCT/conch_v15/20x/part-00002.parquet",
242
- "data/TCGA-TGCT/conch_v15/20x/part-00003.parquet"
243
  ]
244
  }
245
  },
246
- "TCGA-STAD": {
247
  "conch_v15": {
248
- "20x": [
249
- "data/TCGA-STAD/conch_v15/20x/part-00000.parquet",
250
- "data/TCGA-STAD/conch_v15/20x/part-00001.parquet",
251
- "data/TCGA-STAD/conch_v15/20x/part-00002.parquet",
252
- "data/TCGA-STAD/conch_v15/20x/part-00003.parquet"
253
  ]
254
  }
255
  },
256
- "TCGA-THYM": {
257
  "conch_v15": {
258
- "20x": [
259
- "data/TCGA-THYM/conch_v15/20x/part-00000.parquet",
260
- "data/TCGA-THYM/conch_v15/20x/part-00001.parquet",
261
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223
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240
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