imaging-data-commons — Удобный доступ к медицинским изображениям рака

--- name: imaging-data-commons description: Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses. 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: 1.4.0 skill-author: Andrey Fedorov, @fedorov idc-index: "0.11.10" idc-data-version: "v23" repository: https://github.com/ImagingDataCommons/idc-claude-skill --- # Imaging Data Commons ## Overview 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 needed (run this FIRST):** ```python import idc_index REQUIRED_VERSION = "0.11.10" # Must match metadata.idc-index in this file installed = idc_index.__version__ if installed < REQUIRED_VERSION: print(f"Upgrading idc-index from {installed} to {REQUIRED_VERSION}...") import subprocess subprocess.run(["pip3", "install", "--upgrade", "--break-system-packages", "idc-index"], check=True) print("Upgrade complete. Restart Python to use new version.") else: print(f"idc-index {installed} meets requirement ({REQUIRED_VERSION})") ``` **Verify IDC data version and check current data scale:** ```python from idc_index import IDCClient client = IDCClient() # Verify IDC data version (should be "v23") print(f"IDC data version: {client.get_idc_version()}") # 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) | ## 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 `collection_id` to find original imaging data, may include annotations deposited along with the images; use `analysis_result_id` to find AI-generated or expert 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. **Complete index table documentation:** Use https://idc-index.readthedocs.io/en/latest/indices_reference.html for quick check of available tables and columns without executing any code. **Important:** Use `client.indices_overview` to get current table descriptions and column schemas. This is the authoritative source for available columns and their types — always query it when writing SQL or exploring data structure. ### Available Tables | Table | Row Granularity | Loaded | Description | |-------|-----------------|--------|-------------| | `index` | 1 row = 1 DICOM series | Auto | Primary metadata for all current IDC data | | `prior_versions_index` | 1 row = 1 DICOM series | Auto | Series from previous IDC releases; for downloading deprecated data | | `collections_index` | 1 row = 1 collection | fetch_index() | Collection-level metadata and descriptions | | `analysis_results_index` | 1 row = 1 analysis result collection | fetch_index() | Metadata about derived datasets (annotations, segmentations) | | `clinical_index` | 1 row = 1 clinical data column | fetch_index() | Dictionary mapping clinical table columns to collections | | `sm_index` | 1 row = 1 slide microscopy series | fetch_index() | Slide Microscopy (pathology) series metadata | | `sm_instance_index` | 1 row = 1 slide microscopy instance | fetch_index() | Instance-level (SOPInstanceUID) metadata for slide microscopy | | `seg_index` | 1 row = 1 DICOM Segmentation series | fetch_index() | Segmentation metadata: algorithm, segment count, reference to source image series | | `ann_index` | 1 row = 1 DICOM ANN series | fetch_index() | Microscopy Bulk Simple Annotations series metadata; references annotated image series | | `ann_group_index` | 1 row = 1 annotation group | fetch_index() | Detailed annotation group metadata: graphic type, annotation count, property codes, algorithm | | `contrast_index` | 1 row = 1 series with contrast info | fetch_index() | Contrast agent metadata: agent name, ingredient, administration route (CT, MR, PT, XA, RF) | **Auto** = loaded automatically when `IDCClient()` is instantiated **fetch_index()** = requires `client.fetch_index("table_name")` to load ### Joining Tables **Key columns are not explicitly labeled, the following is a subset that can be used in joins.** | Join Column | Tables | Use Case | |-------------|--------|----------| | `collection_id` | index, prior_versions_index, collections_index, clinical_index | Link series to collection metadata or clinical data | | `SeriesInstanceUID` | index, prior_versions_index, sm_index, sm_instance_index | Link series across tables; connect to slide microscopy details | | `StudyInstanceUID` | index, prior_versions_index | Link studies across current and historical data | | `PatientID` | index, prior_versions_index | Link patients across current and historical 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 | | `crdc_series_uuid` | index, prior_versions_index | Link by CRDC unique identifier | | `Modality` | index, prior_versions_index | Filter by imaging modality | | `SeriesInstanceUID` | index, seg_index, ann_index, ann_group_index, contrast_index | Link segmentation/annotation/contrast series to its index metadata | | `segmented_SeriesInstanceUID` | seg_index → index | Link segmentation to its source image series (join seg_index.segmented_SeriesInstanceUID = index.SeriesInstanceUID) | | `referenced_SeriesInstanceUID` | ann_index → index | Link annotation to its source image series (join ann_index.referenced_SeriesInstanceUID = index.SeriesInstanceUID) | **Note:** `Subjects`, `Updated`, and `Description` appear in multiple tables but have different meanings (counts vs identifiers, different update contexts). For detailed join examples, schema discovery patterns, key columns reference, and DataFrame access, see `references/index_tables_guide.md`. ### Clinical Data Access ```python # Fetch clinical index (also downloads clinical data tables) client.fetch_index("clinical_index") # Query clinical index to find available tables and their columns tables = client.sql_query("SELECT DISTINCT table_name, column_label FROM clinical_index") # Load a specific clinical table as DataFrame clinical_df = client.get_clinical_table("table_name") ``` See `references/clinical_data_guide.md` for detailed workflows including value mapping patterns and joining clinical data with imaging. ## Data Access Options | Method | Auth Required | Best For | |--------|---------------|----------| | `idc-index` | No | Key queries and downloads (recommended) | | IDC Portal | No | Interactive exploration, manual selection, browser-based download | | BigQuery | Yes (GCP account) | Complex queries, full DICOM metadata | | DICOMweb proxy | No | Tool integration via DICOMweb API | | Cloud storage (S3/GCS) | No | Direct file access, bulk downloads, custom pipelines | **Cloud storage organization** IDC maintains all DICOM files in public cloud storage buckets mirrored between AWS S3 and Google Cloud Storage. Files are organized by CRDC UUIDs (not DICOM UIDs) to support versioning. | Bucket (AWS / GCS) | License | Content | |--------------------|---------|---------| | `idc-open-data` / `idc-open-data` | No commercial restriction | >90% of IDC data | | `idc-open-data-two` / `idc-open-idc1` | No commercial restriction | Collections with potential head scans | | `idc-open-data-cr` / `idc-open-cr` | Commercial use restricted (CC BY-NC) | ~4% of data | Files are stored as `<crdc_series_uuid>/<crdc_instance_uuid>.dcm`. Access is free (no egress fees) via AWS CLI, gsutil, or s5cmd with anonymous access. Use `series_aws_url` column from the index for S3 URLs; GCS uses the same path structure. See `references/cloud_storage_guide.md` for bucket details, access commands, UUID mapping, and versioning. **DICOMweb access** IDC data is available via DICOMweb interface (Google Cloud Healthcare API implementation) for integration with PACS systems and DICOMweb-compatible tools. | Endpoint | Auth | Use Case | |----------|------|----------| | Public proxy | No | Testing, moderate queries, daily quota | | Google Healthcare | Yes (GCP) | Production use, higher quotas | See `references/dicomweb_guide.md` for endpoint URLs, code examples, supported operations, and implementation details. ## Installation and Setup **Required (for basic access):** ```bash pip install --upgrade idc-index ``` **Important:** New IDC data release will always trigger a new version of `idc-index`. Always use `--upgrade` flag while installing, unless an older version is needed for reproducibility. **IMPORTANT:** IDC data version v23 is current. Always verify your version: ```python print(client.get_idc_version()) # Should return "v23" ``` If you see an older version, upgrade with: `pip install --upgrade idc-index` **Tested with:** idc-index 0.11.10 (IDC data version v23) **Optional (for data analysis):** ```bash pip install pandas numpy pydicom ``` ## Core Capabilities ### 1. Data Discovery and Exploration Discover what imaging collections and data are available in IDC: ```python from idc_index import IDCClient client = IDCClient() # Get summary statistics from primary index query = """ SELECT collection_id, COUNT(DISTINCT PatientID) as patients, COUNT(DISTINCT SeriesInstanceUID) as series, SUM(series_size_MB) as size_mb FROM index GROUP BY collection_id ORDER BY patients DESC """ collections_summary = client.sql_query(query) # For richer collection metadata, use collections_index client.fetch_index("collections_index") collections_info = client.sql_query(""" SELECT collection_id, CancerTypes, TumorLocations, Species, Subjects, SupportingData FROM collections_index """) # For analysis results (annotations, segmentations), use analysis_results_index client.fetch_index("analysis_results_index") analysis_info = client.sql_query(""" SELECT analysis_result_id, analysis_result_title, Subjects, Collections, Modalities FROM analysis_results_index """) ``` **`collections_index`** provides curated metadata per collection: cancer types, tumor locations, species, subject counts, and supporting data types — without needing to aggregate from the primary index. **`analysis_results_index`** lists derived datasets (AI segmentations, expert annotations, radiomics features) with their source collections and modalities. ### 2. Querying Metadata with SQL Query the IDC mini-index using SQL to find specific datasets. **First, explore available values for filter columns:** ```python from idc_index import IDCClient client = IDCClient() # Check what Modality values exist modalities = client.sql_query(""" SELECT DISTINCT Modality, COUNT(*) as series_count FROM index GROUP BY Modality ORDER BY series_count DESC """) print(modalities) # Check what BodyPartExamined values exist for MR modality body_parts = client.sql_query(""" SELECT DISTINCT BodyPartExamined, COUNT(*) as series_count FROM index WHERE Modality = 'MR' AND BodyPartExamined IS NOT NULL GROUP BY BodyPartExamined ORDER BY series_count DESC LIMIT 20 """) print(body_parts) ``` **Then query with validated filter values:** ```python # Find breast MRI scans (use actual values from exploration above) results = client.sql_query(""" SELECT collection_id, PatientID, SeriesInstanceUID, Modality, SeriesDescription, license_short_name FROM index WHERE Modality = 'MR' AND BodyPartExamined = 'BREAST' LIMIT 20 """) # Access results as pandas DataFrame for idx, row in results.iterrows(): print(f"Patient: {row['PatientID']}, Series: {row['SeriesInstanceUID']}") ``` **To filter by cancer type, join with `collections_index`:** ```python client.fetch_index("collections_index") results = client.sql_query(""" SELECT i.collection_id, i.PatientID, i.SeriesInstanceUID, i.Modality FROM index i JOIN collections_index c ON i.collection_id = c.collection_id WHERE c.CancerTypes LIKE '%Breast%' AND i.Modality = 'MR' LIMIT 20 """) ``` **Available metadata fields** (use `client.indices_overview` for complete list): - Identifiers: collection_id, PatientID, StudyInstanceUID, SeriesInstanceUID - Imaging: Modality, BodyPartExamined, Manufacturer, ManufacturerModelName - Clinical: PatientAge, PatientSex, StudyDate - Descriptions: StudyDescription, SeriesDescription - Licensing: license_short_name **Note:** Cancer type is in `collections_index.CancerTypes`, not in the primary `index` table. ### 3. Downloading DICOM Files Download imaging data efficiently from IDC's cloud storage: **Download entire collection:** ```python from idc_index import IDCClient client = IDCClient() # Download small collection (RIDER Pilot ~1GB) client.download_from_selection( collection_id="rider_pilot", downloadDir="./data/rider" ) ``` **Download specific series:** ```python # First, query for series UIDs series_df = client.sql_query(""" SELECT SeriesInstanceUID FROM index WHERE Modality = 'CT' AND BodyPartExamined = 'CHEST' AND collection_id = 'nlst' LIMIT 5 """) # Download only those series client.download_from_selection( seriesInstanceUID=list(series_df['SeriesInstanceUID'].values), downloadDir="./data/lung_ct" ) ``` **Custom directory structure:** Default `dirTemplate`: `%collection_id/%PatientID/%StudyInstanceUID/%Modality_%SeriesInstanceUID` ```python # Simplified hierarchy (omit StudyInstanceUID level) client.download_from_selection( collection_id="tcga_luad", downloadDir="./data", dirTemplate="%collection_id/%PatientID/%Modality" ) # Results in: ./data/tcga_luad/TCGA-05-4244/CT/ # Flat structure (all files in one directory) client.download_from_selection( seriesInstanceUID=list(series_df['SeriesInstanceUID'].values), downloadDir="./data/flat", dirTemplate="" ) # Results in: ./data/flat/*.dcm ``` **Downloaded file names:** Individual DICOM files are named using their CRDC instance UUID: `<crdc_instance_uuid>.dcm` (e.g., `0d73f84e-70ae-4eeb-96a0-1c613b5d9229.dcm`). This UUID-based naming: - Enables version tracking (UUIDs change when file content changes) - Matches cloud storage organization (`s3://idc-open-data/<crdc_series_uuid>/<crdc_instance_uuid>.dcm`) - Differs from DICOM UIDs (SOPInstanceUID) which are preserved inside the file metadata To identify files, use the `crdc_instance_uuid` column in queries or read DICOM metadata (SOPInstanceUID) from the files. ### Command-Line Download The `idc download` command provides command-line access to download functionality without writing Python code. Available after installing `idc-index`. **Auto-detects input type:** manifest file path, or identifiers (collection_id, PatientID, StudyInstanceUID, SeriesInstanceUID, crdc_series_uuid). ```bash # Download entire collection idc download rider_pilot --download-dir ./data # Download specific series by UID idc download "1.3.6.1.4.1.9328.50.1.69736" --download-dir ./data # Download multiple items (comma-separated) idc download "tcga_luad,tcga_lusc" --download-dir ./data # Download from manifest file (auto-detected) idc download manifest.txt --download-dir ./data ``` **Options:** | Option | Description | |--------|-------------| | `--download-dir` | Output directory (default: current directory) | | `--dir-template` | Directory hierarchy template (default: `%collection_id/%PatientID/%StudyInstanceUID/%Modality_%SeriesInstanceUID`) | | `--log-level` | Verbosity: debug, info, warning, error, critical | **Manifest files:** Manifest files contain S3 URLs (one per line) and can be: - Exported from the IDC Portal after cohort selection - Shared by collaborators for reproducible data access - Generated programmatically from query results Format (one S3 URL per line): ``` s3://idc-open-data/cb09464a-c5cc-4428-9339-d7fa87cfe837/* s3://idc-open-data/88f3990d-bdef-49cd-9b2b-4787767240f2/* ``` **Example: Generate manifest from Python query:** ```python from idc_index import IDCClient client = IDCClient() # Query for series URLs results = client.sql_query(""" SELECT series_aws_url FROM index WHERE collection_id = 'rider_pilot' AND Modality = 'CT' """) # Save as manifest file with open('ct_manifest.txt', 'w') as f: for url in results['series_aws_url']: f.write(url + 'n') ``` Then download: ```bash idc download ct_manifest.txt --download-dir ./ct_data ``` ### 4. Visualizing IDC Images View DICOM data in browser without downloading: ```python from idc_index import IDCClient import webbrowser client = IDCClient() # First query to get valid UIDs results = client.sql_query(""" SELECT SeriesInstanceUID, StudyInstanceUID FROM index WHERE collection_id = 'rider_pilot' AND Modality = 'CT' LIMIT 1 """) # View single series viewer_url = client.get_viewer_URL(seriesInstanceUID=results.iloc[0]['SeriesInstanceUID']) webbrowser.open(viewer_url) # View all series in a study (useful for multi-series exams like MRI protocols) viewer_url = client.get_viewer_URL(studyInstanceUID=results.iloc[0]['StudyInstanceUID']) webbrowser.open(viewer_url) ``` The method automatically selects OHIF v3 for radiology or SLIM for slide microscopy. Viewing by study is useful when a DICOM Study contains multiple Series (e.g., T1, T2, DWI sequences from a single MRI session). ### 5. Understanding and Checking Licenses Check data licensing before use (critical for commercial applications): ```python from idc_index import IDCClient client = IDCClient() # Check licenses for all collections query = """ SELECT DISTINCT collection_id, license_short_name, COUNT(DISTINCT SeriesInstanceUID) as series_count FROM index GROUP BY collection_id, license_short_name ORDER BY collection_id """ licenses = client.sql_query(query) print(licenses) ``` **License types in IDC:** - **CC BY 4.0** / **CC BY 3.0** (~97% of data) - Allows commercial use with attribution - **CC BY-NC 4.0** / **CC BY-NC 3.0** (~3% of data) - Non-commercial use only - **Custom licenses** (rare) - Some collections have specific terms (e.g., NLM Terms and Conditions) **Important:** Always check the license before using IDC data in publications or commercial applications. Each DICOM file is tagged with its specific license in metadata. ### Generating Citations for Attribution The `source_DOI` column contains DOIs linking to publications describing how the data was generated. To satisfy attribution requirements, use `citations_from_selection()` to generate properly formatted citations: ```python from idc_index import IDCClient client = IDCClient() # Get citations for a collection (APA format by default) citations = client.citations_from_selection(collection_id="rider_pilot") for citation in citations: print(citation) # Get citations for specific series results = client.sql_query(""" SELECT SeriesInstanceUID FROM index WHERE collection_id = 'tcga_luad' LIMIT 5 """) citations = client.citations_from_selection( seriesInstanceUID=list(results['SeriesInstanceUID'].values) ) # Alternative format: BibTeX (for LaTeX documents) bibtex_citations = client.citations_from_selection( collection_id="tcga_luad", citation_format=IDCClient.CITATION_FORMAT_BIBTEX ) ``` **Parameters:** - `collection_id`: Filter by collection(s) - `patientId`: Filter by patient ID(s) - `studyInstanceUID`: Filter by study UID(s) - `seriesInstanceUID`: Filter by series UID(s) - `citation_format`: Use `IDCClient.CITATION_FORMAT_*` constants: - `CITATION_FORMAT_APA` (default) - APA style - `CITATION_FORMAT_BIBTEX` - BibTeX for LaTeX - `CITATION_FORMAT_JSON` - CSL JSON - `CITATION_FORMAT_TURTLE` - RDF Turtle **Best practice:** When publishing results using IDC data, include the generated citations to properly attribute the data sources and satisfy license requirements. ### 6. Batch Processing and Filtering Process large datasets efficiently with filtering: ```python from idc_index import IDCClient import pandas as pd client = IDCClient() # Find chest CT scans from GE scanners 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 later 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}" ) ``` ### 7. Advanced Queries with BigQuery For queries requiring full DICOM metadata, complex JOINs, clinical data tables, or private DICOM elements, use Google BigQuery. Requires GCP account with billing enabled. **Quick reference:** - Dataset: `bigquery-public-data.idc_current.*` - Main table: `dicom_all` (combined metadata) - Full metadata: `dicom_metadata` (all DICOM tags) - Private elements: `OtherElements` column (vendor-specific tags like diffusion b-values) See `references/bigquery_guide.md` for setup, table schemas, query patterns, private element access, and cost optimization. **Before using BigQuery**, always check if a specialized index table already has the metadata you need: 1. Use `client.indices_overview` or the [idc-index indices reference](https://idc-index.readthedocs.io/en/latest/indices_reference.html) to discover all available tables and their columns 2. Fetch the relevant index: `client.fetch_index("table_name")` 3. Query locally with `client.sql_query()` (free, no GCP account needed) Common specialized indices: `seg_index` (segmentations), `ann_index` / `ann_group_index` (microscopy annotations), `sm_index` (slide microscopy), `collections_index` (collection metadata). Only use BigQuery if you need private DICOM elements or attributes not in any index. ### 8. Tool Selection Guide | Task | Tool | Reference | |------|------|-----------| | Programmatic queries & downloads | `idc-index` | This document | | Interactive exploration | IDC Portal | https://portal.imaging.datacommons.cancer.gov/ | | Complex metadata queries | BigQuery | `references/bigquery_guide.md` | | 3D visualization & analysis | SlicerIDCBrowser | https://github.com/ImagingDataCommons/SlicerIDCBrowser | **Default choice:** Use `idc-index` for most tasks (no auth, easy API, batch downloads). ### 9. Integration with Analysis Pipelines Integrate IDC data into imaging analysis workflows: **Read downloaded DICOM files:** ```python import pydicom import os # Read DICOM files from downloaded series 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')] # Load first image 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}") ``` **Build 3D volume from CT series:** ```python import pydicom import numpy as np from pathlib import Path def load_ct_series(series_path): """Load CT series as 3D numpy array""" files = sorted(Path(series_path).glob('*.dcm')) slices = [pydicom.dcmread(str(f)) for f in files] # Sort by slice location slices.sort(key=lambda x: float(x.ImagePositionPatient[2])) # Stack into 3D array volume = np.stack([s.pixel_array for s in slices]) return volume, slices[0] # Return volume and first slice for metadata volume, metadata = load_ct_series("./data/lung_ct/series_dir") print(f"Volume shape: {volume.shape}") # (z, y, x) ``` **Integrate with SimpleITK:** ```python import SimpleITK as sitk from pathlib import Path # Read DICOM series series_path = "./data/ct_series" reader = sitk.ImageSeriesReader() dicom_names = reader.GetGDCMSeriesFileNames(series_path) reader.SetFileNames(dicom_names) image = reader.Execute() # Apply processing smoothed = sitk.CurvatureFlow(image1=image, timeStep=0.125, numberOfIterations=5) # Save as NIfTI sitk.WriteImage(smoothed, "processed_volume.nii.gz") ``` ## Common Use Cases See `references/use_cases.md` for complete end-to-end workflow examples including: - Building deep learning training datasets from lung CT scans - Comparing image quality across scanner manufacturers - Previewing data in browser before downloading - License-aware batch downloads for commercial use ## Best Practices - **Verify IDC version before generating responses** - Always call `client.get_idc_version()` at the start of a session to confirm you're using the expected data version (currently v23). If using an older version, recommend `pip install --upgrade idc-index` - **Check licenses before use** - Always query the `license_short_name` field and respect licensing terms (CC BY vs CC BY-NC) - **Generate citations for attribution** - Use `citations_from_selection()` to get properly formatted citations from `source_DOI` values; include these in publications - **Start with small queries** - Use `LIMIT` clause when exploring to avoid long downloads and understand data structure - **Use mini-index for simple queries** - Only use BigQuery when you need comprehensive metadata or complex JOINs - **Organize downloads with dirTemplate** - Use meaningful directory structures like `%collection_id/%PatientID/%Modality` - **Cache query results** - Save DataFrames to CSV files to avoid re-querying and ensure reproducibility - **Estimate size first** - Check collection size before downloading - some collection sizes are in terabytes! - **Save manifests** - Always save query results with Series UIDs for reproducibility and data provenance - **Read documentation** - IDC data structure and metadata fields are documented at https://learn.canceridc.dev/ - **Use IDC forum** - Search for questons/answers and ask your questions to the IDC maintainers and users at https://discourse.canceridc.dev/ ## Troubleshooting **Issue: `ModuleNotFoundError: No module named 'idc_index'`** - **Cause:** idc-index package not installed - **Solution:** Install with `pip install --upgrade idc-index` **Issue: Download fails with connection timeout** - **Cause:** Network instability or large download size - **Solution:** - Download smaller batches (e.g., 10-20 series at a time) - Check network connection - Use `dirTemplate` to organize downloads by batch - Implement retry logic with delays **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 current IDC version, or wrong field name - **Solution:** - Check if data is in current IDC version (some old data may be deprecated) - Use `LIMIT 5` to test query first - Check field names against metadata schema documentation **Issue: Downloaded DICOM files won't open** - **Cause:** Corrupted download or incompatible viewer - **Solution:** - Check DICOM object type (Modality and SOPClassUID attributes) - some object types require specialized tools - Verify file integrity (check file sizes) - Use pydicom to validate: `pydicom.dcmread(file, force=True)` - Try different DICOM viewer (3D Slicer, Horos, RadiAnt, QuPath) - Re-download the series ## Common SQL Query Patterns See `references/sql_patterns.md` for quick-reference SQL patterns including: - Filter value discovery (modalities, body parts, manufacturers) - Annotation and segmentation queries (including seg_index, ann_index joins) - Slide microscopy queries (sm_index patterns) - Download size estimation - Clinical data linking For segmentation and annotation details, also see `references/digital_pathology_guide.md`. ## Related Skills The following skills complement IDC workflows for downstream analysis and visualization: ### DICOM Processing - **pydicom** - Read, write, and manipulate downloaded DICOM files. Use for extracting pixel data, reading metadata, anonymization, and format conversion. Essential for working with IDC radiology data (CT, MR, PET). ### Pathology and Slide Microscopy See `references/digital_pathology_guide.md` for DICOM-compatible tools (highdicom, wsidicom, TIA-Toolbox, Slim viewer). ### Metadata Visualization - **matplotlib** - Low-level plotting for full customization. Use for creating static figures summarizing IDC query results (bar charts of modalities, histograms of series counts, etc.). - **seaborn** - Statistical visualization with pandas integration. Use for quick exploration of IDC metadata distributions, relationships between variables, and categorical comparisons with attractive defaults. - **plotly** - Interactive visualization. Use when you need hover info, zoom, and pan for exploring IDC metadata, or for creating web-embeddable dashboards of collection statistics. ### Data Exploration - **exploratory-data-analysis** - Comprehensive EDA on scientific data files. Use after downloading IDC data to understand file structure, quality, and characteristics before analysis. ## Resources ### Schema Reference (Primary Source) **Always use `client.indices_overview` for current column schemas.** This ensures accuracy with the installed idc-index version: ```python # Get all column names and types for any table schema = client.indices_overview["index"]["schema"] columns = [(c['name'], c['type'], c.get('description', '')) for c in schema['columns']] ``` ### Reference Documentation See the Quick Navigation section at the top for the full list of reference guides with decision triggers. - **[indices_reference](https://idc-index.readthedocs.io/en/latest/indices_reference.html)** - External documentation for index tables (may be ahead of the installed version) ### External Links - **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 GitHub**: https://github.com/ImagingDataCommons/idc-index - **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 This skill version is available in skill metadata. To check for updates: - Visit the [releases page](https://github.com/ImagingDataCommons/idc-claude-skill/releases) - Watch the repository on GitHub (Watch → Custom → Releases)