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v1.4.0

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@fedorov fedorov released this 04 Mar 22:17
· 49 commits to main since this release
v1.4.0
4a51999

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

Changed

  • Updated to idc-index 0.11.10 (adds ContainerIdentifier column to sm_index)
  • Updated sm_index table description to reflect newly available columns (container/slide ID, tissue type, anatomic structure, diagnosis)

Full Changelog: v1.3.1...v1.4.0

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