公开癌症影像查询与研究

references/use_cases.md

Tested with: idc-index 0.12.5 (IDC data version v24)

These download and local-file processing examples are illustrative; metadata queries were smoke-tested with the pinned IDC release. This guide provides end-to-end workflow examples for common IDC use cases. Each use case demonstrates the full workflow from query to download with best practices.

When to Use This Guide

Load this guide when you need:

• Complete end-to-end workflow examples for training dataset creation
• Patterns for multi-step data selection and download workflows
• Examples of license-aware data handling for commercial use
• Visualization workflows for data preview before download

For core API patterns (query, download, visualize, citations), see the "Core Capabilities" section in the main SKILL.md.

Prerequisites

Needs idc-index installed — run python scripts/check_version.py, which reports the installed version and prints the install command for the interpreter you are running.

Use Case 1: Find and Download Lung CT Scans for Deep Learning

Objective: Build training dataset of lung CT scans from NLST collection

Steps:

from idc_index import IDCClient

client = IDCClient()

# 1. Query for lung CT scans with specific criteria
query = """
SELECT
  PatientID,
  SeriesInstanceUID,
  SeriesDescription,
  crdc_series_uuid, series_aws_url, license_short_name, source_DOI
FROM index
WHERE collection_id = 'nlst'
  AND Modality = 'CT'
  AND BodyPartExamined = 'CHEST'
  AND license_short_name = 'CC BY 4.0'
ORDER BY PatientID
LIMIT 100
"""

results = client.sql_query(query)
print(f"Found {len(results)} series from {results['PatientID'].nunique()} patients")

# 2. Download data organized by patient
client.download_from_selection(
    seriesInstanceUID=list(results['SeriesInstanceUID'].values),
    downloadDir="./training_data",
    dirTemplate="%collection_id/%PatientID/%SeriesInstanceUID"
)

# 3. Save manifest for reproducibility
results.to_csv('training_manifest.csv', index=False)

Use Case 2: Query Brain MRI by Manufacturer for Quality Study

Objective: Compare image quality across different MRI scanner manufacturers

Steps:

from idc_index import IDCClient
import pandas as pd

client = IDCClient()

# Query for brain MRI grouped by manufacturer
query = """
SELECT
  Manufacturer,
  ManufacturerModelName,
  COUNT(DISTINCT SeriesInstanceUID) as num_series,
  COUNT(DISTINCT PatientID) as num_patients
FROM index
WHERE Modality = 'MR'
  AND BodyPartExamined LIKE '%BRAIN%'
GROUP BY Manufacturer, ManufacturerModelName
HAVING num_series >= 10
ORDER BY num_series DESC
"""

manufacturers = client.sql_query(query)
print(manufacturers)

# Download sample from each manufacturer for comparison
for _, row in manufacturers.head(3).iterrows():
    mfr = row['Manufacturer']
    model = row['ManufacturerModelName']

    # Use DataFrame equality to handle quotes and missing values in vendor strings.
    series = client.index[
        client.index['Manufacturer'].eq(mfr) &
        client.index['ManufacturerModelName'].eq(model) &
        client.index['Modality'].eq('MR') &
        client.index['BodyPartExamined'].str.contains('BRAIN', na=False)
    ].head(5)
    client.download_from_selection(
        seriesInstanceUID=list(series['SeriesInstanceUID'].values),
        downloadDir=f"./quality_study/{mfr.replace(' ', '_')}"
    )

Use Case 3: Visualize Series Without Downloading

Objective: Preview imaging data before committing to download

from idc_index import IDCClient
import webbrowser

client = IDCClient()

series_list = client.sql_query("""
    SELECT SeriesInstanceUID, PatientID, SeriesDescription
    FROM index
    WHERE collection_id = 'acrin_nsclc_fdg_pet' AND Modality = 'PT'
    LIMIT 10
""")

# Preview each in browser
for _, row in series_list.iterrows():
    viewer_url = client.get_viewer_URL(seriesInstanceUID=row['SeriesInstanceUID'])
    print(f"Patient {row['PatientID']}: {row['SeriesDescription']}")
    print(f"  View at: {viewer_url}")
    # webbrowser.open(viewer_url)  # Uncomment to open automatically

For additional visualization options, see the IDC Portal getting started guide or SlicerIDCBrowser for 3D Slicer integration.

Use Case 4: License-Aware Batch Download for Commercial Use

Objective: Download only CC-BY licensed data suitable for commercial applications

Steps:

from idc_index import IDCClient

client = IDCClient()

# Query ONLY for CC BY licensed data (allows commercial use with attribution)
query = """
SELECT
  SeriesInstanceUID,
  collection_id,
  PatientID,
  Modality,
  crdc_series_uuid, series_aws_url, license_short_name, source_DOI
FROM index
WHERE license_short_name IN ('CC BY 3.0', 'CC BY 4.0')
  AND Modality IN ('CT', 'MR')
  AND BodyPartExamined IN ('CHEST', 'BRAIN', 'ABDOMEN')
LIMIT 200
"""

cc_by_data = client.sql_query(query)

print(f"Found {len(cc_by_data)} CC BY licensed series")
print(f"Collections: {cc_by_data['collection_id'].unique()}")

# Download with license verification
client.download_from_selection(
    seriesInstanceUID=list(cc_by_data['SeriesInstanceUID'].values),
    downloadDir="./commercial_dataset",
    dirTemplate="%collection_id/%Modality/%PatientID/%SeriesInstanceUID"
)

# Save license information
cc_by_data.to_csv('commercial_dataset_manifest_CC-BY_ONLY.csv', index=False)

Use Case 5: Batch Download with Filtering

Objective: Download a large filtered dataset in batches to avoid timeouts

Steps:

from idc_index import IDCClient
import pandas as pd

client = IDCClient()

# Find chest CT scans from GE scanners with a permissive license
query = """
SELECT
  SeriesInstanceUID,
  PatientID,
  collection_id,
  ManufacturerModelName
FROM index
WHERE Modality = 'CT'
  AND BodyPartExamined = 'CHEST'
  AND Manufacturer = 'GE MEDICAL SYSTEMS'
  AND license_short_name = 'CC BY 4.0'
LIMIT 100
"""

results = client.sql_query(query)

# Save manifest for reproducibility
results.to_csv('lung_ct_manifest.csv', index=False)

# Download in batches to avoid timeout
batch_size = 10
for i in range(0, len(results), batch_size):
    batch = results.iloc[i:i+batch_size]
    client.download_from_selection(
        seriesInstanceUID=list(batch['SeriesInstanceUID'].values),
        downloadDir=f"./data/batch_{i//batch_size}"
    )

Use Case 6: Integration with Analysis Pipelines

Objective: Load downloaded DICOM files into Python for processing

Read individual DICOM files with pydicom:

import pydicom
import os

series_dir = "./data/rider/rider_pilot/RIDER-1007893286/CT_1.3.6.1..."

dicom_files = [os.path.join(series_dir, f) for f in os.listdir(series_dir)
               if f.endswith('.dcm')]

ds = pydicom.dcmread(dicom_files[0])
print(f"Patient ID: {ds.PatientID}")
print(f"Modality: {ds.Modality}")
print(f"Image shape: {ds.pixel_array.shape}")

Load one conventional CT series with SimpleITK:

This example requires local DICOM files and is illustrative. Use volume_geometry_index to screen candidates, then check orientation, spacing, missing/duplicate slices, and pixel units in the actual files. Sorting only ImagePositionPatient[2] is wrong for oblique or sagittal series, and raw pixel_array values are not automatically Hounsfield units.

import SimpleITK as sitk

series_path = "./data/ct_series"
series_ids = sitk.ImageSeriesReader.GetGDCMSeriesIDs(series_path)
if len(series_ids) != 1:
    raise ValueError(f"Select exactly one CT series; found {len(series_ids)}")
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(series_path, series_ids[0])
reader.SetFileNames(dicom_names)
image = reader.Execute()
print(image.GetSize(), image.GetSpacing(), image.GetDirection())
# Confirm CT rescale/unit semantics before treating intensities as HU.
image = sitk.Cast(image, sitk.sitkFloat32)
smoothed = sitk.CurvatureFlow(image1=image, timeStep=0.125, numberOfIterations=5)
sitk.WriteImage(smoothed, "processed_volume.nii.gz")

For ML datasets, split by patient (and where needed institution), keep all studies and series from one patient in the same split, and document collection/label provenance. Selecting 100 series is not equivalent to selecting 100 independent patients.

Resources

• Main SKILL.md for core API patterns (query, download, visualize)
• references/clinical_data_guide.md for clinical data integration workflows
• references/sql_patterns.md for additional SQL query patterns
• references/index_tables_guide.md for complex join patterns