Data & ReproScientific VisualizationK-Dense-AI/claude-scientific-skillsData & Reproduction

Data Commons

Maintainer Andrey Fedorov, @fedorov · Last updated April 1, 2026

Use the `idc-index` Python package to query and download public cancer imaging data from the National Cancer Institute Imaging Data Commons (IDC). No authentication required for data access. **Current IDC Data Version: v23** (always verify with `IDCClient().get_idc_version()`) **Primary tool:** `idc-index` ([GitHub](https://github.com/imagingdatacommons/idc-index)) **CRITICAL - Check package version and upgrade if n….

Claude CodeOpenClawNanoClawAnalysisWritingimaging-data-commonsdata-analysispackagedata analysis & visualization

Original source

K-Dense-AI/claude-scientific-skills

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/imaging-data-commons

Maintainer: Andrey Fedorov, @fedorov
License: 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.
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Use the idc-index Python package to query and download public cancer imaging data from the National Cancer Institute Imaging Data Commons (IDC). No authentication required for data access.
Current IDC Data Version: v23 (always verify with IDCClient().get_idc_version()).
Primary tool: idc-index (GitHub).
CRITICAL - Check package version and upgrade if needed (run this FIRST):.
Verify IDC data version and check current data scale:.

Source Doc

Excerpt From SKILL.md

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) |

Use cases

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.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Related skills

Back to directory

Data & ReproScientific Visualization

bgpt-paper-search

BGPT is a remote MCP server that searches a curated database of scientific papers built from raw experimental data extracted from full-text…

Claude CodeOpenClawAnalysis

K-Dense-AI/claude-scientific-skillsView

Data & ReproScientific Visualization

bio-chipseq-visualization

Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal a…

OpenClawNanoClawAnalysis

FreedomIntelligence/OpenClaw-Medical-SkillsView

Data & ReproScientific Visualization

bio-consensus-sequences

Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific refer…

OpenClawNanoClawAnalysis

FreedomIntelligence/OpenClaw-Medical-SkillsView

Data & ReproScientific Visualization

bio-copy-number-cnv-visualization

Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or oth…

OpenClawNanoClawAnalysis

FreedomIntelligence/OpenClaw-Medical-SkillsView