| --- |
| license: cc-by-sa-4.0 |
| license_link: https://creativecommons.org/licenses/by-sa/4.0/ |
| task_categories: |
| - image-classification |
| - video-classification |
| - object-detection |
| tags: |
| - medical |
| - cystoscopy |
| - bladder-cancer |
| - histopathology |
| - endoscopy |
| language: |
| - en |
| pretty_name: Cystoscopy Core Benchmark |
| size_categories: |
| - 1K<n<10K |
| --- |
| |
| # Cystoscopy Core Benchmark |
|
|
| Raw-source core dataset for cystoscopy image and video classification. Contains |
| cystoscopy videos with bounding-box annotations, and images with lesion-level |
| labels, grades, and stages. Designed as the source-of-truth from which derived |
| training datasets (v1, v2, G) are built. |
|
|
| ## Sources |
|
|
| The dataset aggregates three publicly available cystoscopy datasets: |
|
|
| | Source | Origin | Modality | Patients | Images/Frames | Type | |
| |--------|--------|----------|----------|---------------|------| |
| | B | B_dataset | Video clips (CLARA+CHROMA / white light) | 30 | 173 videos (2448 annotated frames) | Track clips with bounding boxes | |
| | C | CystoDS | Still images (WLC / BLC) | 160 | 8067 images | Histopathology-confirmed stills | |
| | D | Lazo et al. | Still images (WLI / NBI) | 22 | 1754 images | Histopathology-confirmed stills | |
| |
| ## Dataset Structure |
| |
| ``` |
| cystoscopy-core/ |
| ├── data/ |
| │ ├── image_annotations.parquet # 12,269 rows: per-image labels, grade, stage, segmentation |
| │ ├── video_annotations.parquet # 173 rows: per-video metadata (histological type, grade, stage) |
| │ └── video_frame_boxes.parquet # 69,108 rows: per-frame bounding boxes (x,y,w,h) |
| ├── B/videos/ # 173 .mp4 video clips (1920x1080) |
| ├── C/images/<pid>/ # 8067 .png images organized by patient |
| └── D/images/<pid>/ # 1754 .png images organized by patient |
| ``` |
| |
| ## Annotation Schemas |
| |
| ### image_annotations.parquet (12,269 rows) |
|
|
| Per-image annotation table covering all C images, all D images, and B video |
| frames selected for the G-derived benchmark. |
|
|
| | Column | Type | Description | |
| |--------|------|-------------| |
| | `source_dataset` | string | B, C, or D | |
| | `patient_id` | int | Normalized patient ID (B: 1–30, C: 31–190, D: 191–212) | |
| | `lesion_id` | string | Lesion grouping (B: `B_<track>_<idx>`, C: `L0`–`L6`/`Multifocal`, D: `D_<case>_pt<pt>_<tissue>`) | |
| | `filename` | string | Image filename (C/D only; B uses video_id + frame_idx) | |
| | `label` | int | 0 = malignant tumor (MT), 1 = non-malignant lesion (NML), 2 = non-ROI (NROI) | |
| | `grade` | string | `low`, `high`, or null (inferred from histological type / subclass / tissue type) | |
| | `stage` | string | `Ta`, `T1`, `Tis`, `T2`, or null (D has no stage) | |
| | `subclass` | string | Source-native subclass (C: LowGradePapillary, HighGradePapillary, CIS, etc.) | |
| | `subclass2` | string | Secondary reclassification (C only; 16 rows) | |
| | `morphology` | string | C: Papillary, Non-papillary, etc. | |
| | `visit` | float | C: visit number | |
| | `multifocal` | string | C: multifocal flag | |
| | `imaging_type` | string | Unified modality (CLARA + CHROMA, white light, WLC, BLC, WLI, NBI) | |
| | `segmentation` | list | Polygon segmentation masks (C only; 768 of 8,067 images) | |
| | `video_id` | string | B: video clip identifier (e.g., P017_cystoscopy_track_077) | |
| | `frame_idx` | float | B: frame index within video clip | |
|
|
| ### video_annotations.parquet (173 rows) |
| |
| | Column | Type | Description | |
| |--------|------|-------------| |
| | `video_id` | string | Video clip identifier | |
| | `patient_id` | int | Normalized patient ID | |
| | `histological_type` | string | pTaLG, pT1LG, pTaHG, pT1HG, pT2HG, pT2, PUNLMP | |
| | `light_mode` | string | CLARA + CHROMA or white light | |
| | `num_frames` | int | Actual frame count of the .mp4 file (not original cystoscopy length) | |
| | `n_boxes` | int | Number of bounding boxes in this video | |
| | `stage` | string | Ta, T1, T2 (derived from histological_type) | |
| | `grade` | string | low, high, or null (pT2 and PUNLMP → null) | |
| | `imaging_type` | string | Same as light_mode for B | |
| |
| ### video_frame_boxes.parquet (69,108 rows) |
| |
| | Column | Type | Description | |
| |--------|------|-------------| |
| | `video_id` | string | Video clip identifier | |
| | `patient_id` | int | Normalized patient ID | |
| | `track_id` | int | Track number within patient | |
| | `frame` | int | Frame index within video clip (0-indexed) | |
| | `label` | string | Box label (all "tumor"; class comes from video-level histological_type) | |
| | `xtl`, `ytl`, `xbr`, `ybr` | float | Bounding box coordinates (pixels, 1920x1080) | |
| | `occluded` | int | Occlusion flag | |
| | `outside` | int | Outside frame flag | |
| | `keyframe` | int | Keyframe flag | |
| | `z_order` | int | Z-order for overlap resolution | |
|
|
| ## Label Distribution (image_annotations) |
| |
| | Label | ID | Count | |
| |-------|----|-------| |
| | Malignant Tumor (MT) | 0 | 4,512 | |
| | Non-Malignant Lesion (NML) | 1 | 355 | |
| | Non-ROI (NROI) | 2 | 7,402 | |
| | **Total** | | **12,269** | |
| |
| ## Grade Distribution |
| |
| | Grade | Count | |
| |-------|-------| |
| | Low | 2,633 | |
| | High | 1,888 | |
| |
| ## Stage Distribution |
| |
| | Stage | Count | |
| |-------|-------| |
| | Ta | 2,017 | |
| | T1 | 1,124 | |
| | Tis | 71 | |
| | T2 | 261 | |
| |
| ## Histological Type Distribution (B videos) |
| |
| | Type | Count | |
| |------|-------| |
| | Urothelial carcinoma pTaLG | 77 | |
| | Urothelial carcinoma pT1LG | 38 | |
| | Urothelial carcinoma pT1HG | 27 | |
| | PUNLMP | 12 | |
| | Urothelial carcinoma pTaHG | 8 | |
| | Urothelial carcinoma pT2HG | 7 | |
| | Urothelial carcinoma pT2 | 4 | |
| |
| ## Patient IDs |
| |
| Normalized mapping (1-indexed): |
| - B: patients 1–30 (30 patients, 173 video track clips) |
| - C: patients 31–190 (160 patients, 8067 images) |
| - D: patients 191–212 (22 patients, 1754 images) |
| |
| ## Licensing |
| |
| This is a mixed-license dataset: |
| - **Source B**: CC BY 4.0 |
| - **Source C (CystoDS)**: CC BY 4.0 |
| - **Source D (Lazo et al.)**: CC BY-SA 4.0 |
| |
| The combined dataset is distributed under CC BY-SA 4.0 (the most restrictive |
| component license). |
| |
| ## Citation |
| |
| If you use this dataset, please cite the original source datasets. |
| |
| ## Usage |
| |
| ```python |
| from datasets import load_dataset |
| from huggingface_hub import hf_hub_download |
| |
| # Load annotation tables |
| ds = load_dataset("milkyroad/cystoscopy-core") |
|
|
| # Download a specific image |
| hf_hub_download( |
| repo_id="milkyroad/cystoscopy-core", |
| filename="C/images/P031/d6df5610.png", |
| repo_type="dataset", |
| ) |
| |
| # Download a specific video |
| hf_hub_download( |
| repo_id="milkyroad/cystoscopy-core", |
| filename="B/videos/P000_cystoscopy_track_000.mp4", |
| repo_type="dataset", |
| ) |
| ``` |
| |
