| --- |
| pretty_name: OpenThyroidDB |
| language: |
| - en |
| - zh |
| task_categories: |
| - image-segmentation |
| - image-classification |
| - object-detection |
| - image-to-text |
| tags: |
| - medical-imaging |
| - ultrasound |
| - thyroid |
| - multicenter |
| - report-generation |
| --- |
| |
| # OpenThyroidDB |
|
|
| **A multicenter, multitask thyroid ultrasound data resource supporting the ThyroidXAgent evidence workflow.** |
|
|
| OpenThyroidDB integrates curated public thyroid ultrasound resources and institutionally governed clinical cohorts into a full-spectrum resource for **segmentation**, **benign–malignant classification**, **report generation**, and **malignant-lesion stratification** across diverse scanners and acquisition settings. |
|
|
| This Hugging Face repository (`MedXAgent/OpenThyroidDB`) is the data-distribution layer of OpenThyroidDB. It separates redistributed or processed external resources from MedXAgent-governed cohorts, while preserving dataset-level provenance and archive boundaries. |
|
|
|
|
| ## Scope of the resource |
|
|
| The task organization follows Figure 1 of the ThyroidXAgent study: |
|
|
| | Task | Evidence represented in the current repository | Primary use | |
| |---|---|---| |
| | **Segmentation** | CineClip, TGVideo, ThyroidXL, TN3K, PKTN, DDTI, TN5000 masks, TNVideo | Pixel-/region-level delineation of thyroid structures and lesions | |
| | **Classification** | AHU, ThyroidXL, ThyUS2Path, TN5000/TN5K, TN3K, DDTI, TNVideo | Thyroid nodule diagnosis and categorization | |
| | **Report generation** | KMVE, SMU-HMC, ZJH-TS, TNVideo | Standardized report generation from ultrasound images or videos | |
| | **Malignant-lesion stratification** | Supporting thyroid image resources and task-specific ThyroidXAgent cohorts | FTC/PTC prediction and lymph-node-metastasis subtype classification | |
|
|
| Figure 1 reports task-specific curated subsets rather than raw archive totals. Examples include: |
|
|
| - **Public segmentation resources:** CineClip (17,417), TGVideo (15,186), ThyroidXL (11,631), TN3K (5,347), PKTN (1,003), and DDTI (637 images). |
| - **Public classification resources:** AHU (125,896), ThyroidXL (11,631), ThyUS2Path (8,508), TN5K (5,000), TN3K (5,347), and DDTI (349 images). |
| - **Report-generation resources:** KMVE (2,474 reports / 15,921 images), SMU-HMC (23,955 reports / 248,194 images), ZJH-TS (353 reports / 4,471 images), and a TNVideo report-generation subset (145 case videos). |
| - **TNVideo task subsets:** 148 cases for segmentation/classification and 145 case videos for report generation in the paper workflow. |
|
|
|
|
| ## Scanner and acquisition diversity |
|
|
| OpenThyroidDB spans still images, cine clips, videos, masks, bounding boxes, categorical labels, and free-text reports collected across heterogeneous acquisition environments. Scanner families represented in the study include, among others: |
|
|
| - GE LOGIQ E9 and GE S7 |
| - Fujifilm ARIETTA 850 and Hitachi Aloka ARIETTA V70 |
| - Mindray RESONA 70B |
| - Toshiba Nemio 30 / Nemio MX |
| - Esaote MyLab |
| - Samsung Medison RS80 |
| - SuperSonic Imagine Aixplorer Ultimate |
|
|
| Scanner availability and metadata completeness vary by source dataset. |
|
|
| ## Current repository structure |
|
|
| The layout below reflects the current Hugging Face release: |
|
|
| ```text |
| OpenThyroidDB/ |
| ├── ExternalDatasets/ |
| │ ├── AHU/ |
| │ │ └── AHU-ProcessedData.zip |
| │ ├── CineClip/ |
| │ │ └── Cine-clip.zip |
| │ ├── DDTI/ |
| │ │ ├── DDTI_SourceData.zip |
| │ │ └── DDTI_processed.zip |
| │ ├── KMVE/ |
| │ │ └── KMVE.zip |
| │ ├── PKTN/ |
| │ │ └── PKTN.zip |
| │ ├── TG3K/ |
| │ │ └── tg3k.zip |
| │ ├── TGVideo/ |
| │ │ └── TGVideo.zip |
| │ ├── TN3K/ |
| │ │ └── TN3K.zip |
| │ ├── TN5000/ |
| │ │ ├── TN5000.zip |
| │ │ └── TN5K_MASK_SAM2_L.zip |
| │ ├── ThyUS2Path/ |
| │ │ └── ThyUS2Path.zip |
| │ ├── ThyroidXL/ |
| │ │ └── ThyroidXL.zip |
| │ └── ZJH-2K/ |
| │ └── ZJH-2K.zip |
| └── MedXAgentDatasets/ |
| ├── SMU-HMC/ |
| │ ├── Batch1.zip ... Batch15.zip |
| │ ├── Batch_Multiple_Cases.zip |
| │ └── test_set_single.json |
| ├── TNVideo/ |
| │ ├── SourceVideoAndAnno.zip |
| │ ├── VIDEO_DATASET.zip |
| │ └── VIDEO_ImageAndMask.zip |
| └── ZJH-TS/ |
| ├── ZJH-TS.zip |
| └── test_150cases_manifest.csv |
| ``` |
|
|
| ## Released components |
|
|
| ### ExternalDatasets |
|
|
| `ExternalDatasets/` contains source-aligned or processed archives derived from publicly described datasets. Each subdirectory is kept separate to make provenance, licensing, and citation easier to audit. |
|
|
| | Directory | Current archive(s) | Main task relevance | |
| |---|---|---| |
| | `AHU/` | `AHU-ProcessedData.zip` | Classification | |
| | `CineClip/` | `Cine-clip.zip` | Segmentation, classification | |
| | `DDTI/` | `DDTI_SourceData.zip`, `DDTI_processed.zip` | Segmentation, classification | |
| | `KMVE/` | `KMVE.zip` | Report generation | |
| | `PKTN/` | `PKTN.zip` | Segmentation | |
| | `TG3K/` | `tg3k.zip` | Thyroid ultrasound image analysis | |
| | `TGVideo/` | `TGVideo.zip` | Video/frame segmentation | |
| | `TN3K/` | `TN3K.zip` | Segmentation, classification | |
| | `TN5000/` | `TN5000.zip`, `TN5K_MASK_SAM2_L.zip` | Detection/classification and derived SAM2 masks | |
| | `ThyUS2Path/` | `ThyUS2Path.zip` | Classification | |
| | `ThyroidXL/` | `ThyroidXL.zip` | Segmentation, classification, detection | |
| | `ZJH-2K/` | `ZJH-2K.zip` | Thyroid ultrasound image analysis | |
|
|
| Users must consult and cite the original publication and license for every external dataset they use. Inclusion in this repository does not relicense an external resource. |
|
|
| ### MedXAgentDatasets |
|
|
| `MedXAgentDatasets/` contains institutionally governed or MedXAgent-curated releases used by the ThyroidXAgent workflow. |
|
|
| #### SMU-HMC |
|
|
| - Multicenter image–report cohort for thyroid ultrasound report generation. |
| - The paper cohort contains **23,955 reports and 248,194 images**. |
| - The current release is distributed as 15 batch archives, an additional multiple-case archive, and `test_set_single.json`. |
|
|
| #### ZJH-TS |
|
|
| - De-identified thyroid ultrasound image–report cohort. |
| - Full archive: **353 reports and 4,471 images**. |
| - `test_150cases_manifest.csv` provides the final selected evaluation subset of **150 reports and 2,034 images**. |
| - Manifest columns are `index`, `report_id`, `data_dir`, `n_images`, `findings`, `impression`, and `time`. |
|
|
| #### TNVideo |
|
|
| - Thyroid ultrasound video resource supporting segmentation, classification, and video-conditioned report generation. |
| - `SourceVideoAndAnno.zip`: source videos and sparse frame-level annotations. |
| - `VIDEO_ImageAndMask.zip`: extracted images and masks. |
| - `VIDEO_DATASET.zip`: processed video-oriented release. |
| - Frame annotations in the source archive are sparse Pascal VOC bounding boxes rather than dense per-frame segmentation masks. |
|
|
| ## Access, governance, and responsible use |
|
|
| By requesting or using this repository, users agree to: |
|
|
| 1. Use the data only for legitimate research, education, and method development permitted by the applicable source terms. |
| 2. Respect the original licenses, citations, and redistribution restrictions of all external datasets. |
| 3. Follow the approved access conditions for institutionally governed cohorts. |
| 4. Not attempt to identify or contact any individual represented in the data. |
| 5. Not use the repository as a substitute for clinical judgment or as a clinically validated diagnostic product. |
| 6. Apply appropriate security, ethics, and institutional review procedures when handling downloaded data. |
|
|
|
|
| ## Download |
|
|
| Authenticate and request access on the dataset page before downloading gated files: |
|
|
| ```bash |
| hf auth login |
| ``` |
|
|
| Download a specific component: |
|
|
| ```bash |
| hf download MedXAgent/OpenThyroidDB \ |
| "MedXAgentDatasets/ZJH-TS/ZJH-TS.zip" \ |
| --repo-type dataset |
| ``` |
|
|
| Download a directory with Python: |
|
|
| ```python |
| from huggingface_hub import snapshot_download |
| |
| snapshot_download( |
| repo_id="MedXAgent/OpenThyroidDB", |
| repo_type="dataset", |
| allow_patterns=["MedXAgentDatasets/ZJH-TS/*"], |
| local_dir="OpenThyroidDB", |
| ) |
| ``` |
|
|
|
|
