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README.md

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+---
+license: cc-by-nc-nd-4.0
+tags:
+- histopathology
+- whole-slide-image
+---
+
+# BigCell sample data
+
+This is a small sample of the data format used to train and evaluate
+[BigCell](https://huggingface.co/StonyBrook-CVLab/BigCell) ([GitHub](https://github.com/cvlab-stonybrook/BigCell)).
+It contains two 32,768×32,768 regions at 20×:
+
+| Region | Source |
+|---|---|
+| `cptac/AML/C3L-00453-41_x0_y0` | CPTAC (AML) |
+| `tcga_diagnostic/brca/TCGA-3C-AALI-01Z-00-DX1.F6E9A5DF-D8FB-45CF-B4BD-C6B76294C291_x0_y0` | TCGA-BRCA (diagnostic) |
+
+Each region is cut into non-overlapping crops of 2048 to 32768 px, excluding background. The sample has
+6.8 GB, 1,600 files.
+
+## Layout
+
+All crops are at 20×. `<size>` is the side length of the crop in pixels at 20×.
+
+```
+<source>/<type>/<slide>_x<X>_y<Y>/<size>/      size ∈ {2048, 4096, 8192, 16384, 32768}
+    <N>.jpg          2048×2048 image (the crop downsampled when size > 2048)
+    <N>_full.jpg     the crop at full resolution (size > 2048)
+    <N>_uni.npy      (size/256, size/256, 1536) float16 UNI-2h grid, one token per 256×256 patch
+    <N>_vae.npy      (64, 256, 256) float16 FLUX.2 VAE posterior mean ‖ std of <N>.jpg
+metadata/
+    image_list_train.h5      datasets size_<size>: relative paths of every <N>.jpg
+    new_organ_split.csv      organ ↔ (source, type) used in the paper
+image_embedding_stats/uni2_{4096,8192}/normalization_stats.pt
+                             per-position mean / var of UNI-2 grids over the full training set (used by the CGM)
+```
+
+| size | crops | used for |
+|---|---|---|
+| 2048 | 367 | training the tile generator (`_vae.npy` + `_uni.npy`) |
+| 4096 / 8192 | 93 / 24 | CGM training grids; 4k / 8k generation |
+| 16384 / 32768 | 7 / 2 | 16k / 32k generation |
+
+## Usage
+
+```bash
+huggingface-cli download StonyBrook-CVLab/BigCell-sample-data --repo-type dataset --local-dir bigcell_sample_data
+
+# generate an 8192×8192 image from a real region's UNI-2 grid
+python scripts/generate_from_grid.py --grid bigcell_sample_data/cptac/AML/C3L-00453-41_x0_y0/8192/0_uni.npy --out 8k.jpg
+
+# fine-tune the 2048 tile generator on the sample
+torchrun --nproc_per_node 4 -m bigcell.train configs/bigcell/2048.yaml --data-dir bigcell_sample_data \
+    --init-from bigcell-2048 --batch-size 8 --max-train-steps 100
+```
+
+The TITAN report embeddings that the CGM is trained on are not part of this sample.
+
+## License
+
+CC BY-NC-ND 4.0. The images derive from CPTAC and TCGA, which are subject to their original data-use terms. The
+UNI-2h features and FLUX.2 latents are subject to the licences of those models.

cptac/AML/C3L-00453-41_x0_y0/2048/110_uni.npy

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metadata/new_organ_split.csv

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+Category,Dataset,Folder_Name
+Breast,cptac,brca
+Breast,gtex,Breast - Mammary Tissue
+Breast,histai,Breast
+Breast,others,ACROBAT
+Breast,tcga_diagnostic,brca
+Breast,tcga_fresh_frozen,brca
+Endocrine,gtex,Adrenal Gland
+Endocrine,gtex,Pituitary
+Endocrine,gtex,Thyroid
+Endocrine,histai,Endocrine
+Endocrine,tcga_diagnostic,acc
+Endocrine,tcga_diagnostic,pcpg
+Endocrine,tcga_diagnostic,thca
+Endocrine,tcga_fresh_frozen,acc
+Endocrine,tcga_fresh_frozen,pcpg
+Endocrine,tcga_fresh_frozen,thca
+Gastrointestinal,cptac,PDA
+Gastrointestinal,cptac,coad
+Gastrointestinal,gtex,Colon - Sigmoid
+Gastrointestinal,gtex,Colon - Transverse
+Gastrointestinal,gtex,Esophagus - Gastroesophageal Junction
+Gastrointestinal,gtex,Esophagus - Mucosa
+Gastrointestinal,gtex,Esophagus - Muscularis
+Gastrointestinal,gtex,Liver
+Gastrointestinal,gtex,Pancreas
+Gastrointestinal,gtex,Small Intestine - Terminal Ileum
+Gastrointestinal,gtex,Stomach
+Gastrointestinal,histai,Gastrointestinal
+Gastrointestinal,tcga_diagnostic,chol
+Gastrointestinal,tcga_diagnostic,coad
+Gastrointestinal,tcga_diagnostic,esca
+Gastrointestinal,tcga_diagnostic,lihc
+Gastrointestinal,tcga_diagnostic,paad
+Gastrointestinal,tcga_diagnostic,read
+Gastrointestinal,tcga_diagnostic,stad
+Gastrointestinal,tcga_fresh_frozen,chol
+Gastrointestinal,tcga_fresh_frozen,coad
+Gastrointestinal,tcga_fresh_frozen,esca
+Gastrointestinal,tcga_fresh_frozen,lihc
+Gastrointestinal,tcga_fresh_frozen,paad
+Gastrointestinal,tcga_fresh_frozen,read
+Gastrointestinal,tcga_fresh_frozen,stad
+Genitourinary,cptac,CCRCC
+Genitourinary,gtex,Bladder
+Genitourinary,gtex,Kidney - Cortex
+Genitourinary,gtex,Kidney - Medulla
+Genitourinary,gtex,Prostate
+Genitourinary,gtex,Testis
+Genitourinary,histai,Genitourinary
+Genitourinary,others,PANDA
+Genitourinary,tcga_diagnostic,blca
+Genitourinary,tcga_diagnostic,kich
+Genitourinary,tcga_diagnostic,kirc
+Genitourinary,tcga_diagnostic,kirp
+Genitourinary,tcga_diagnostic,prad
+Genitourinary,tcga_diagnostic,tgct
+Genitourinary,tcga_fresh_frozen,blca
+Genitourinary,tcga_fresh_frozen,kich
+Genitourinary,tcga_fresh_frozen,kirc
+Genitourinary,tcga_fresh_frozen,kirp
+Genitourinary,tcga_fresh_frozen,prad
+Genitourinary,tcga_fresh_frozen,tgct
+Gynecologic,gtex,Cervix - Ectocervix
+Gynecologic,gtex,Cervix - Endocervix
+Gynecologic,gtex,Fallopian Tube
+Gynecologic,gtex,Ovary
+Gynecologic,gtex,Uterus
+Gynecologic,gtex,Vagina
+Gynecologic,histai,Gynecologic
+Gynecologic,others,PTRC-HGSOC
+Gynecologic,tcga_diagnostic,cesc
+Gynecologic,tcga_diagnostic,ov
+Gynecologic,tcga_diagnostic,ucec
+Gynecologic,tcga_diagnostic,ucs
+Gynecologic,tcga_fresh_frozen,cesc
+Gynecologic,tcga_fresh_frozen,ov
+Gynecologic,tcga_fresh_frozen,ucec
+Gynecologic,tcga_fresh_frozen,ucs
+Head and Neck,cptac,HNSCC
+Head and Neck,gtex,Minor Salivary Gland
+Head and Neck,histai,Head and Neck
+Head and Neck,tcga_diagnostic,hnsc
+Head and Neck,tcga_fresh_frozen,hnsc
+Hematologic,cptac,AML
+Hematologic,gtex,Spleen
+Hematologic,histai,Hematologic
+Hematologic,tcga_diagnostic,dlbc
+Hematologic,tcga_fresh_frozen,dlbc
+Nervous System,cptac,GBM
+Nervous System,gtex,Brain - Cerebellum
+Nervous System,gtex,Brain - Cortex
+Nervous System,gtex,Nerve - Tibial
+Nervous System,tcga_diagnostic,gbm
+Nervous System,tcga_diagnostic,lgg
+Nervous System,tcga_fresh_frozen,gbm
+Nervous System,tcga_fresh_frozen,lgg
+Other,histai,Other
+Other,tcga_diagnostic,uvm
+Other,tcga_fresh_frozen,uvm
+Skin,cptac,CM
+Skin,gtex,Skin - Not Sun Exposed (Suprapubic)
+Skin,gtex,Skin - Sun Exposed (Lower leg)
+Skin,histai,Skin
+Skin,tcga_diagnostic,skcm
+Skin,tcga_fresh_frozen,skcm
+Soft Tissue,cptac,SAR
+Soft Tissue,gtex,Adipose - Subcutaneous
+Soft Tissue,gtex,Adipose - Visceral (Omentum)
+Soft Tissue,gtex,Artery - Aorta
+Soft Tissue,gtex,Artery - Coronary
+Soft Tissue,gtex,Artery - Tibial
+Soft Tissue,gtex,Muscle - Skeletal
+Soft Tissue,tcga_diagnostic,sarc
+Soft Tissue,tcga_fresh_frozen,sarc
+Thorax,cptac,LSCC
+Thorax,cptac,LUAD
+Thorax,gtex,Heart - Atrial Appendage
+Thorax,gtex,Heart - Left Ventricle
+Thorax,gtex,Lung
+Thorax,histai,Thorax
+Thorax,others,NLST
+Thorax,tcga_diagnostic,luad
+Thorax,tcga_diagnostic,lusc
+Thorax,tcga_diagnostic,meso
+Thorax,tcga_diagnostic,thym
+Thorax,tcga_fresh_frozen,luad
+Thorax,tcga_fresh_frozen,lusc
+Thorax,tcga_fresh_frozen,meso
+Thorax,tcga_fresh_frozen,thym

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