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README.md
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- name: ymin
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dtype: int32
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splits:
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- name: train
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num_bytes: 4910314207
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num_examples: 151
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download_size: 4910506566
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dataset_size: 4910314207
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configs:
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- config_name: default
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data_files:
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- split: train
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path: data/train-*
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---
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---
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license: cc0-1.0
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task_categories:
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- image-segmentation
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tags:
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- medical
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- pathology
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- h-and-e
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- breast
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- segmentation
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- bcss
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size_categories:
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- n<1K
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---
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# BCSS — Breast Cancer Semantic Segmentation (Amgad et al. 2019)
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Re-hosted mirror of the **Breast Cancer Semantic Segmentation** dataset
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(Amgad et al., *Bioinformatics* 2019), originally distributed via the
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[PathologyDataScience/BCSS](https://github.com/PathologyDataScience/BCSS)
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GitHub repo and rebuilt here from the
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[`nabil-m/bcss`](https://huggingface.co/datasets/nabil-m/bcss) HF mirror.
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The data is **CC0 1.0** (public domain, no rights reserved); the upstream
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codebase is MIT-licensed but covers software, not data. Redistribution is
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unrestricted.
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## Composition
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| Split | ROIs |
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|-------|-----:|
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| train | 151 |
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151 ROI patches extracted from TCGA breast cancer whole-slide images.
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Patches are **color-normalized** RGB at the upstream MPP=0.25 µm/px
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(40× equivalent), with native ROI resolution typically 2–4k px per
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side. There is **no official train/val/test split** — group-shuffle by
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`patient_id` downstream for honest evaluation.
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## Schema
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| Column | Type | Description |
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|-------------|----------|-------------------------------------------------------|
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| `image` | `Image` | RGB ROI (PNG, color-normalized, variable size) |
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| `mask` | `Image` | Indexed 22-class mask (`L`, values 0..21) |
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| `image_id` | `string` | Filename stem incl. xmin/ymin |
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| `patient_id`| `string` | TCGA-XX-YYYY prefix |
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| `xmin` | `int32` | ROI bbox xmin in WSI base-magnification pixels |
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| `ymin` | `int32` | ROI bbox ymin in WSI base-magnification pixels |
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## Mask labels
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| Code | Class | | Code | Class |
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|-----:|------------------------|-|-----:|----------------------|
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| 0 | outside_roi (don't care) | | 11 | other_immune_infiltrate |
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| 1 | tumor | | 12 | mucoid_material |
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| 2 | stroma | | 13 | normal_acinus_or_duct |
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| 3 | lymphocytic_infiltrate | | 14 | lymphatics |
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| 4 | necrosis_or_debris | | 15 | undetermined |
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| 5 | glandular_secretions | | 16 | nerve |
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| 6 | blood | | 17 | skin_adnexa |
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| 7 | exclude | | 18 | blood_vessel |
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| 8 | metaplasia_NOS | | 19 | angioinvasion |
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| 9 | fat | | 20 | dcis |
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| 10 | plasma_cells | | 21 | other |
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**Code 0 (`outside_roi`) is a "don't care" region** — the original paper
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recommends excluding it from any loss. For binary tumor evaluation,
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the canonical foreground is class 1.
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## License
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CC0 1.0 Universal — public domain. No rights reserved.
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## Citation
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```bibtex
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@article{amgad2019structured,
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title = {Structured crowdsourcing enables convolutional segmentation of histology images},
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author = {Amgad, Mohamed and Elfandy, Habiba and Hussein, Hagar and others},
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journal = {Bioinformatics},
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volume = {35},
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number = {18},
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pages = {3461--3467},
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year = {2019},
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doi = {10.1093/bioinformatics/btz083}
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}
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```
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