Imaging Data Commons

---
name: imaging-data-commons
description: Query and download public cancer imaging data from NCI Imaging Data Commons. Invoke for any question about IDC collections, cancer imaging datasets, DICOM data access, radiology (CT, MR, PET) or pathology AI training sets, metadata queries, visualization, or license checks — even when the user doesn't explicitly mention "IDC". No authentication required.
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.
metadata:
  version: '1.5'
  category: scientific-databases
  maintainer: Kalaris Labs
  source-skill-version: 1.8.1
  idc-index: 0.12.5
  idc-data-version: v24
  repository: https://github.com/ImagingDataCommons/imaging-data-commons-skill
  contributor: Andrey Fedorov, @fedorov
---

# Imaging Data Commons

## Overview

Query and download public cancer imaging data from the National Cancer Institute Imaging Data Commons (IDC). No authentication required for data access.

**Expected network access:** IDC metadata is reachable three ways — a local DuckDB index shipped with the `idc-index` Python package (no network), or the hosted IDC service over MCP or REST (`api.imaging.datacommons.cancer.gov`, no authentication). File downloads use public GCS (`storage.googleapis.com`) and AWS S3 (`s3.amazonaws.com`) — no authentication required. DICOMweb access uses either the public IDC proxy (`proxy.imaging.datacommons.cancer.gov`, no auth) or the Google Cloud Healthcare API (`healthcare.googleapis.com`, requires GCP authentication). Optional BigQuery queries (`bigquery.googleapis.com`) also require GCP authentication. No credentials or environment variables are accessed by this skill.

**Current IDC Data Version: v24** (always verify — see *Best Practices*)

**Choose the access path first.** There is no single default: the cheapest correct path depends
on the session and the task.

1. **Session already has the IDC MCP server?** Route discovery and metadata there — see *IDC
   MCP Server*.
2. **Otherwise, is `idc-index` installed?** Run `python scripts/check_version.py`. If it passes,
   use `idc-index` for everything.
3. **Not installed, and the task is read-only metadata** — counts, attribute values, collection
   lookups, SQL under 10 000 rows, licenses, citations, viewer URLs? **Use the REST API over
   `curl`; do not install anything.** Installing costs ~77 MB of packaged index data plus
   pandas, pyarrow, and duckdb, which a metadata question does not need. See *Data Access
   Options*.
4. **Not installed, and the task needs more than metadata** — downloading files, pandas or
   plotting, pydicom/SimpleITK, pathology tiling, results past 10 000 rows, or a version-pinned
   script the user re-runs? Install `idc-index`: `check_version.py` exits non-zero and prints
   the exact install command for the running interpreter. Prefer a virtual environment, then
   restart Python.

`idc-index` ([GitHub](https://github.com/imagingdatacommons/idc-index)) is still the most
capable path and the only one that moves image bytes; the rule is just not to pay for it before
the task calls for it. `check_version.py` never installs anything itself — it also flags a newer
`idc-index` or skill release when one exists.

**Setup for the `idc-index` path:**

```python
from idc_index import IDCClient
client = IDCClient()

# Verify IDC data version (should be "v24")
print(f"IDC data version: {client.get_idc_version()}")
```

**Core workflow:** query metadata with `client.sql_query()` → download with
`client.download_from_selection()` → visualize with `client.get_viewer_URL()`. Python examples
below assume this `client`; *Data Access Options* has the REST equivalents. For current data
scale, run the summary query in `references/sql_patterns.md` or `GET /v3/stats`.

## IDC MCP Server

IDC operates a hosted MCP server at `https://api.imaging.datacommons.cancer.gov/mcp`
(streamable HTTP, no authentication). Where it is available it complements — it does not
replace — the `idc-index` workflow below.

**Identify it** by the MCP resource `idc://guide`, or by three or more of the tool names
`build_cohort`, `get_cohort_urls`, `list_analysis_results`, and `get_idc_version`. Generic
names such as `run_sql` are not evidence on their own. If identification is ambiguous, use
`idc-index`.

**If this session has the server**, treat it as authoritative for discovery and metadata —
IDC version, counts, attribute values, cohort building, metadata SQL — and follow the
server's own instructions rather than re-deriving them from this file. Its data version is
whatever the server reports: call `get_idc_version` instead of relying on the version pinned
in this file.

Return here for what the server does not do: downloading files, local pandas/notebook
analysis, DICOMweb, BigQuery, digital pathology tiling, and reproducible scripts. Hand off by
passing SeriesInstanceUIDs from the server to `client.download_from_selection(...)`, and run
`scripts/check_version.py` at that point.

**If it is not available**, the identical service is reachable with no configuration as a REST
API at `https://api.imaging.datacommons.cancer.gov/v3` — use it for read-only metadata rather
than installing `idc-index`, per the routing gate in *Overview*. Suggest connecting the MCP
server at most once, only for repeated interactive discovery, and never change the user's
configuration yourself.

See `references/mcp_guide.md` for the tool inventory, handoff patterns, and per-host notes.

## 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

Inline below: the MCP/REST routing rules, the IDC data model, the index tables and how they
join, the core API patterns (query, download, visualize, license, cite), best practices, and
troubleshooting.

**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 workflows: training datasets, batch downloads, DICOM reading with pydicom/SimpleITK, pipeline integration |
| `sql_patterns.md` | Quick SQL patterns for filter discovery, annotations, size estimation |
| `clinical_data_guide.md` | Clinical/tabular data, imaging+clinical joins, value mapping |
| `licensing_and_citation.md` | Commercial-use questions, mixed-license cohorts, citation formats |
| `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) |
| `parquet_access_guide.md` | Direct Parquet queries via GCS (no idc-index install needed) |
| `mcp_guide.md` | Hosted IDC MCP server: tool inventory, identification, handoff to `idc-index` |
| `rest_api_guide.md` | Hosted IDC REST API: endpoints, filter syntax, SQL over HTTP, manifests |

## IDC Data Model

IDC adds two grouping levels above the standard DICOM hierarchy (Patient → Study → Series → Instance):

- **collection_id**: Groups patients by disease, modality, or research focus (e.g., `tcga_luad`, `nlst`). A patient belongs to exactly one collection.
- **analysis_result_id**: Identifies derived objects (segmentations, annotations, radiomics features) across one or more original collections. Use it to find AI-generated or expert annotations, while `collection_id` finds original imaging data (which may itself include deposited annotations).

**Key identifiers for queries:**
| Identifier | Scope | Use for |
|------------|-------|---------|
| `collection_id` | Dataset grouping | Filtering by project/study |
| `PatientID` | Patient | Grouping images by patient |
| `StudyInstanceUID` | DICOM study | Grouping of related series, visualization |
| `SeriesInstanceUID` | DICOM series | Grouping of related series, visualization |

## Index Tables

The `idc-index` package provides multiple metadata index tables, accessible via SQL or as pandas DataFrames. The REST API exposes the same tables through `GET /tables` and `POST /sql`.

**Important:** `client.indices_overview` is the authoritative source for current table descriptions, available columns, and their types — query it when writing SQL or exploring data structure. It also answers "which table contains column X"; see `references/index_tables_guide.md` for that search pattern and full schema discovery.

### Available Tables

Always call `client.fetch_index("table_name")` before querying any index table — it is safe and idempotent for all tables, including those loaded automatically at startup.

| Family | Tables | Granularity |
|--------|--------|-------------|
| Core | `index` (primary metadata for all current data), `collections_index`, `analysis_results_index` | series / collection / analysis result |
| Modality acquisition parameters | `ct_index`, `mr_index`, `pt_index`, `contrast_index` | 1 row = 1 series of that modality |
| Derived objects | `seg_index`, `rtstruct_index`, `ann_index`, `ann_group_index` | 1 row = 1 series (or annotation group) |
| Microscopy | `sm_index`, `sm_instance_index` | 1 row = 1 SM series / instance |
| Geometry, clinical, history | `volume_geometry_index`, `clinical_index`, `version_metadata_index`, `prior_versions_index` | see guide |

`references/index_tables_guide.md` has the full inventory with each table's columns and
contents — load it when you need to know what a specialized table actually holds.

**`prior_versions_index` is for reproducibility only.** It contains series permanently *removed*
from IDC, with zero overlap with `index`. Use it only to reproduce work against a prior IDC
version. Do NOT use it for version history or "what's new" questions — those use
`series_init_idc_version` / `series_revised_idc_version` in the main `index` table, which are
not equivalent to this table's `min_idc_version` / `max_idc_version`.

### Joining Tables

**`SeriesInstanceUID` is the universal join key** for all series-level specialized tables: `sm_index`, `sm_instance_index`, `seg_index`, `ann_index`, `ann_group_index`, `contrast_index`, `volume_geometry_index`, `rtstruct_index`, `ct_index`, `mr_index`, `pt_index`. Always join these to `index` on `SeriesInstanceUID`. The exceptions below use different column names.

| Join Column | Tables | Use Case |
|-------------|--------|----------|
| `collection_id` | index, prior_versions_index, collections_index, clinical_index | Link series to collection metadata or clinical data |
| `analysis_result_id` | index, analysis_results_index | Link series to analysis result metadata (annotations, segmentations) |
| `source_DOI` | index, analysis_results_index | Link by publication DOI |
| `segmented_SeriesInstanceUID` | seg_index → index | Link segmentation to its source image series (`seg_index.segmented_SeriesInstanceUID = index.SeriesInstanceUID`) |
| `referenced_SeriesInstanceUID` | ann_index → index, rtstruct_index → index | Link annotation or RTSTRUCT to its source image series |

**Note:** `subjects`, `updated`, and `description` appear in multiple tables but have different meanings (counts vs identifiers, different update contexts). Joining `prior_versions_index` to `index` on `SeriesInstanceUID` always returns zero rows — see the warning above.

For detailed join examples, schema discovery patterns, key columns reference, and DataFrame access, see `references/index_tables_guide.md`.

### Clinical Data Access

Clinical (non-imaging) attributes — staging, demographics, therapy — live in per-collection
tables. `client.fetch_index("clinical_index")` loads the dictionary mapping columns to
collections; `client.get_clinical_table(name)` returns one table as a DataFrame.

See `references/clinical_data_guide.md` for the discovery workflow, coded-value mapping, and
joining clinical data with imaging.

## Data Access Options

| Method | Auth | Best For | Reference |
|--------|------|----------|-----------|
| `idc-index` | No | Downloads, pandas analysis, unbounded queries — the most capable path | This document |
| IDC MCP server | No | Discovery, cohort building, metadata when the session already has it | `mcp_guide.md` |
| IDC REST API | No | Metadata with no install, from any language or shell — the default when `idc-index` is absent | `rest_api_guide.md` |
| Direct Parquet (GCS) | No | Version-pinned queries, or results past the REST row cap | `parquet_access_guide.md` |
| Cloud storage (S3/GCS) | No | Direct file access, bulk transfer, custom pipelines | `cloud_storage_guide.md` |
| DICOMweb via IDC proxy | No | Tool and PACS integration; daily quota, so testing and moderate use | `dicomweb_guide.md` |
| DICOMweb via Google Healthcare | Yes (GCP) | The same DICOMweb API at production volume, without the proxy quota | `dicomweb_guide.md` |
| SlicerIDCBrowser | No | 3D visualization and analysis in 3D Slicer | https://github.com/ImagingDataCommons/SlicerIDCBrowser |
| BigQuery | Yes (GCP) | Full DICOM metadata, private elements, SR measurements — last resort | `bigquery_guide.md` |

**The IDC Portal (https://portal.imaging.datacommons.cancer.gov/) is interactive only** —
browser-based exploration, manual cohort selection, and download. Unlike every option above it
has no programmatic interface, so point a user there to browse or click through data
themselves; never use it as a step in a script or workflow.

**REST API — the no-install metadata path**

`https://api.imaging.datacommons.cancer.gov/v3`, no authentication: discovery, cohort counts and
manifests, read-only SQL, clinical tables, viewer URLs, licenses, citations. It is the same
service as the MCP server over plain HTTP, so it needs no configuration. It never moves image
bytes — switch to `idc-index` to download, to get a DataFrame, or for results past 10 000 rows.

```bash
B=https://api.imaging.datacommons.cancer.gov/v3
curl -s $B/version   # idc_version, idc_index_data_version, api_version
curl -s $B/stats     # collections, patients, studies, series, instances, size_TB
curl -s "$B/attributes/Modality/values?limit=5"   # real filter values, with counts
curl -s $B/sql -H 'content-type: application/json' \
  -d '{"sql":"SELECT collection_id, COUNT(*) n FROM index GROUP BY 1 ORDER BY n DESC LIMIT 3"}'
curl -s $B/cohort/counts -H 'content-type: application/json' \
  -d '{"filters":{"terms":{"collection_id":["rider_pilot"]}}}'
```

**The filter object always goes under `filters`** — on `cohort/counts`, `cohort/manifest`,
`cohort/manifest.txt`, `licenses`, and `citations` alike. A bare filter or an unrecognized key is
a 422 naming the fix; an unfiltered series-enumerating request is a 400, not the whole archive.
Every filtered response echoes `filters_applied` and `warnings` — read them, because they name
any predicate the server dropped. A zero count with empty `warnings` therefore means the filter
matched nothing, not that a value was miscased; miscasing produces a warning that says so.

`POST /sql` takes one read-only `SELECT`/`WITH` over the tables `idc-index` exposes plus
`clinical.<table>`; `max_rows` defaults to 5 000, caps at 10 000, and `truncated` flags clipping.
`GET /attributes` lists the 19 filterable attributes — clinical values, segmented anatomy, and
acquisition parameters are not among them and need SQL. There is no rate limit or quota. **Use
v3 only:** V1 and V2 are superseded and scheduled for shutdown, so port any `/v1/`- or
`Modality_btw`-style example a user brings rather than extending it.

Both sides build on `idc-index-data`, so compare the API's `idc_index_data_version` against local
`idc_index_data.__version__` before mixing them: the **major is the IDC data release** (`24.x.y`
serves `v24`), so differing minor/patch means the series are identical. If the API is a whole
release ahead, `idc-index` **cannot download the extra series** — it silently skips what its own
index does not list — so either upgrade it (run `scripts/check_version.py` for the right command)
or transfer directly from the bucket with `s5cmd --no-sign-request`.

See `references/rest_api_guide.md` for the endpoint reference, filter grounding, limits, and the
manifest-based download flow.

**Cloud storage organization**

All DICOM files live in public buckets mirrored between AWS S3 and GCS, organized by CRDC UUIDs
(not DICOM UIDs) to support versioning, as `<crdc_series_uuid>/<crdc_instance_uuid>.dcm`. Access
is free (no egress fees) via AWS CLI, gsutil, or s5cmd with anonymous access; use the
`series_aws_url` column for S3 URLs. Note that `idc-open-data-cr` / `idc-open-cr` (~4% of data)
is commercial-use restricted (CC BY-NC). See `references/cloud_storage_guide.md` for the full
bucket list and UUID mapping.

**DICOMweb access**

IDC data is available via DICOMweb (Google Cloud Healthcare API) for PACS integration and
DICOMweb-compatible tools: a public proxy (no auth, daily quota) for testing and moderate
queries, or Google Healthcare (GCP auth) for production volumes. See
`references/dicomweb_guide.md`.

**Direct Parquet access**

The idc-index metadata tables are also published as Parquet on a public GCS bucket
(`idc-index-data-artifacts`), queryable with DuckDB or pandas. This needs DuckDB installed
and cannot reach the per-collection clinical tables, so prefer REST `/sql` for ad-hoc metadata;
choose Parquet to pin a data version or for results past the REST row cap. See
`references/parquet_access_guide.md`.

## Core Capabilities

Details, code examples and parameter tables: [references/core-capabilities.md](references/core-capabilities.md). Read it when this step applies.

## Best Practices

- **Check schema before writing queries** — Use `client.get_index_schema('index')` (reads cached metadata, no SQL executed) or `client.indices_overview` to see all available columns and their descriptions. The version-tracking columns `series_init_idc_version` and `series_revised_idc_version` in the main `index` table directly answer "what's new / when was this added" questions without touching `prior_versions_index`.
- **Never use web search for IDC data content questions** - Always query the IDC index directly, via `client.sql_query()` locally or `POST /v3/sql` over HTTP. Web sources (release notes, blog posts, documentation pages) are frequently out of date and will produce incorrect answers. The index is the authoritative source; use it even when web search is available.
- **Verify the IDC data version at the start of a session** - `client.get_idc_version()`, `GET /v3/version`, or the MCP `get_idc_version` tool, depending on the path in use (currently v24). For a stale local index, run `scripts/check_version.py` and use the upgrade command it prints
- **Check licenses and generate citations** - Query `license_short_name` and respect CC BY vs CC BY-NC terms; use `citations_from_selection()` to produce citations from `source_DOI` for publications
- **Explore small, then commit** - Use `LIMIT` (or a low `max_rows`) while exploring, and check collection size before downloading — some collections are terabytes. See `references/cli_guide.md`
- **Keep downloads reproducible** - Organize with `dirTemplate` (e.g. `%collection_id/%PatientID/%Modality`) and save the Series UIDs or manifest behind any dataset you build

## Troubleshooting

**Issue: `ModuleNotFoundError: No module named 'idc_index'`**
- **Cause:** idc-index package not installed
- **Solution:** If the task is read-only metadata, do not install it — use the REST API instead (*Data Access Options*). Otherwise run `scripts/check_version.py` and use the install command it prints, which targets the running interpreter and pins the vetted version. For data analysis also add pandas, numpy, and pydicom (tested with pandas>=1.5, numpy>=1.23, pydicom>=2.3)

**Issue: Download fails with connection timeout**
- **Cause:** Network instability or large download size
- **Solution:** Download in smaller batches (10-20 series); see `references/cli_guide.md` for
  `--use-s5cmd-sync` resume and retry guidance

**Issue: `BigQuery quota exceeded` or billing errors**
- **Cause:** BigQuery requires billing-enabled GCP project
- **Solution:** Use idc-index mini-index for simple queries (no billing required), or see `references/bigquery_guide.md` for cost optimization tips

**Issue: Series UID not found or no data returned**
- **Cause:** Typo in UID, data not in the current IDC version, or wrong field name
- **Solution:** Test with `LIMIT 5` first, check field names against `client.indices_overview`,
  and confirm the series is in the current version (some old data is deprecated)

**Issue: Column not found in `index` table (e.g., `SliceThickness`, `PixelSpacing`, `KVP`, `EchoTime`, `InjectedDose`)**
- **Cause:** The `index` table contains series-level metadata only; modality-specific acquisition and reconstruction parameters live in dedicated tables (`ct_index`, `mr_index`, `pt_index`)
- **Solution:** Search `client.indices_overview` for the column to find its table — the loop is under *Finding which table contains a column* in `references/index_tables_guide.md` — then fetch and join on `SeriesInstanceUID`:
  ```python
  client.fetch_index("ct_index")
  result = client.sql_query("""
      SELECT i.SeriesInstanceUID, i.Modality, c.SliceThickness, c.KVP, c.PixelSpacing_row_mm
      FROM index i
      JOIN ct_index c USING (SeriesInstanceUID)
      WHERE i.collection_id = 'your_collection'
  """)
  ```

**Issue: Downloaded DICOM files won't open**
- **Cause:** Corrupted download, or an object type the viewer does not handle — SEG, RTSTRUCT,
  SR, and slide microscopy all need specialized tools
- **Solution:** Check `Modality` and `SOPClassUID` first, validate with
  `pydicom.dcmread(file, force=True)`, try another viewer (3D Slicer, QuPath for pathology),
  then re-download

## Resources

Reference guides and their decision triggers are listed in *Quick Navigation* above.

- **IDC Portal**: https://portal.imaging.datacommons.cancer.gov/explore/
- **Documentation**: https://learn.canceridc.dev/ — **Tutorials**: https://github.com/ImagingDataCommons/IDC-Tutorials
- **User Forum**: https://discourse.canceridc.dev/ — **idc-index**: https://github.com/ImagingDataCommons/idc-index
- **[indices_reference](https://idc-index.readthedocs.io/en/latest/indices_reference.html)** — external index-table docs (may be ahead of the installed version)
- **Citation**: Fedorov, A., et al. "National Cancer Institute Imaging Data Commons: Toward Transparency, Reproducibility, and Scalability in Imaging Artificial Intelligence." RadioGraphics 43.12 (2023). https://doi.org/10.1148/rg.230180
- **Skill updates**: [releases page](https://github.com/ImagingDataCommons/imaging-data-commons-skill/releases); watch the repository (Watch → Custom → Releases)

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