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v1.3.0

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@fedorov fedorov released this 10 Feb 23:01
· 52 commits to main since this release
v.1.3.0
229b6f9

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

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