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

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",
)