BG
数据与复现
bgpt-paper-search
bgpt-paper-search：BGPT是一个remote MCP server that searches curated database of scientific papers built ，面向 raw experimenta…
K-Dense-AI/claude-scientific-skills查看
数据与复现
DA
Data Commons
维护者 Andrey Fedorov, @fedorov · 最近更新 2026年4月1日
Data Commons：Use `idc-index` Python package to query 、 download public cancer imaging data ，面向 National Cancer Institute Imaging Data Commons (IDC)。 No authentication required ，用于 data access。
原始来源
K-Dense-AI/claude-scientific-skills
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/imaging-data-commons
- 维护者
- Andrey Fedorov, @fedorov
- 许可
- This skill is provided under the MIT License. IDC data itself has individual licensing (mostly CC-BY, some CC-NC) that must be respected when using the data.
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- Use idc-index Python package to query 、 download public cancer imaging data ，面向 National Cancer Institute Imaging Data Commons (IDC). No authentication required ，用于 data access。
- Current IDC Data Version：v23 (always verify ，支持 IDCClient().get_idc_version())。
- Primary tool：idc-index (GitHub)。
- CRITICAL - Check package version 、 upgrade if needed (run this FIRST)：。
- Verify IDC data version 、 check current data scale：。
原始文档
SKILL.md 摘录
Get collection count and total series
stats = client.sql_query(""" SELECT COUNT(DISTINCT collection_id) as collections, COUNT(DISTINCT analysis_result_id) as analysis_results, COUNT(DISTINCT PatientID) as patients, COUNT(DISTINCT StudyInstanceUID) as studies, COUNT(DISTINCT SeriesInstanceUID) as series, SUM(instanceCount) as instances, SUM(series_size_MB)/1000000 as size_TB FROM index """) print(stats)
**Core workflow:**
1. Query metadata → `client.sql_query()`
2. Download DICOM files → `client.download_from_selection()`
3. Visualize in browser → `client.get_viewer_URL(seriesInstanceUID=...)`
## When to Use This Skill
- Finding publicly available radiology (CT, MR, PET) or pathology (slide microscopy) images
- Selecting image subsets by cancer type, modality, anatomical site, or other metadata
- Downloading DICOM data from IDC
- Checking data licenses before use in research or commercial applications
- Visualizing medical images in a browser without local DICOM viewer software
## Quick Navigation
**Core Sections (inline):**
- IDC Data Model - Collection and analysis result hierarchy
- Index Tables - Available tables and joining patterns
- Installation - Package setup and version verification
- Core Capabilities - Essential API patterns (query, download, visualize, license, citations, batch)
- Best Practices - Usage guidelines
- Troubleshooting - Common issues and solutions
**Reference Guides (load on demand):**
| Guide | When to Load |
|-------|--------------|
| `index_tables_guide.md` | Complex JOINs, schema discovery, DataFrame access |
| `use_cases.md` | End-to-end workflow examples (training datasets, batch downloads) |
| `sql_patterns.md` | Quick SQL patterns for filter discovery, annotations, size estimation |
| `clinical_data_guide.md` | Clinical/tabular data, imaging+clinical joins, value mapping |
| `cloud_storage_guide.md` | Direct S3/GCS access, versioning, UUID mapping |
| `dicomweb_guide.md` | DICOMweb endpoints, PACS integration |
| `digital_pathology_guide.md` | Slide microscopy (SM), annotations (ANN), pathology workflows |
| `bigquery_guide.md` | Full DICOM metadata, private elements (requires GCP) |
| `cli_guide.md` | Command-line tools (`idc download`, manifest files) |
适用场景
- Finding publicly available radiology (CT，MR，PET) 或 pathology (slide microscopy) images。
- Selecting image subsets by cancer type，modality，anatomical site，或 other metadata。
- Downloading DICOM data ，面向 IDC。
- Checking data licenses before use in research 或 commercial applications。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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