[1.4.0] - 2026-03-04

Added

• New "Identifying Tumor vs Normal Slides" section in digital pathology guide with two approaches:
  • Structured DICOM tissue type via primaryAnatomicStructureModifier_CodeMeaning (works across all SM collections)
  • TCGA barcode parsing via ContainerIdentifier (TCGA collections only, catches metastatic edge cases)
• TCGA-BRCA worked examples showing tumor vs normal slide counts
• Documentation references to GDC TCGA barcode format and sample type codes
• Specimen preparation query examples: filtering by staining (H&E), embedding medium (FFPE vs frozen), and fixative, with note about array column syntax (array_to_string, list_contains)
• "Finding Pre-Computed Analysis Results" section: discovering derived datasets (nuclei segmentations, TIL maps) via analysis_results_index, with example joining annotations back to source slides
• Note about per-annotation measurements in DICOM ANN objects (extractable via highdicom after download), with link to microscopy_dicom_ann_intro tutorial

[1.3.1] - 2026-02-11

Added

• Automatic idc-index package version check with upgrade prompt before any queries
• Version check compares installed version against metadata.idc-index in frontmatter and triggers pip install --upgrade when outdated

Fixed

• Prevents "table not found" errors when using newer index tables (e.g., contrast_index) with older idc-index versions

Added

• Digital pathology reference guide (references/digital_pathology_guide.md) with SM, ANN, and SEG query patterns, join examples, and pathology tool recommendations
• seg_index coverage in digital pathology guide with cross-domain clarification (SEG used for both radiology and pathology) and query for finding pathology-specific segmentations
• AnnotationGroupLabel filtering examples for finding annotation groups by name
• SM + ANN cross-reference queries showing how to find annotations on slide microscopy images
• Index discovery guidance before BigQuery section to ensure all local indices are checked first
• Documentation for new ann_index and ann_group_index tables (Microscopy Bulk Simple Annotations)
• Example queries for annotation series and annotation group metadata
• Explanation of downloaded DICOM file naming convention (<crdc_instance_uuid>.dcm)
• New reference guides extracted from SKILL.md:
  • references/index_tables_guide.md - Table schemas, DataFrame access, join column reference
  • references/sql_patterns.md - Quick-reference SQL patterns for common queries
  • references/use_cases.md - End-to-end workflow examples
• Quick Navigation section in SKILL.md with decision triggers for when to load each reference
• idc-data-version field in frontmatter metadata
• Documentation for new contrast_index table (contrast bolus metadata for CT, MR, PT, XA, RF series)

Changed

• Updated to idc-index 0.11.9 (IDC data version v23)
• Reduced SKILL.md from 1,245 to 825 lines by extracting secondary content to reference files
• Core Capabilities sections remain inline to ensure correct API pattern usage
• Refactored detailed SM/ANN content from SKILL.md into references/digital_pathology_guide.md, keeping brief summaries with pointers in main skill
• Made IDC version (v23) more prominent in SKILL.md with verification guidance to prevent responses using older versions
• Clarified distinction between index_tables_guide.md (structure/access) and sql_patterns.md (query examples)
  Full Changelog: v1.2.0...v.1.3.0

What's Changed

• Add references for clinical data and DICOM private tags by @fedorov in #7

Full Changelog: v1.1.0...v1.2.0

What's Changed

• Add references for clinical data and DICOM private tags by @fedorov in #7

Full Changelog: v1.1.0...v1.2.0

What's Changed

• add reference guide for idc-index command line tools by @fedorov in #5
• Update dicomweb reference to explain differences between the two endpoints by @fedorov in #1
• Fix SKILL.md frontmatter: move version to metadata by @andinet in #6

New Contributors

• @fedorov made their first contribution in #5
• @andinet made their first contribution in #6

Full Changelog: v1.0.0...v1.1.0

Full Changelog: https://github.com/ImagingDataCommons/idc-claude-skill/commits/v1.0.0