wsi-dicom-annotations

wsi-dicom-annotations provides UI-independent Rust models, readers, writers, and conversion boundaries for DICOM Whole Slide Microscopy derived objects:

• Microscopy Bulk Simple Annotations (ANN)
• Segmentation (SEG)
• Comprehensive 3D Structured Reports (SR)
• Parametric Maps (PM)
• explicitly profiled pathology and QuPath GeoJSON conversion

The default parametric-map feature includes profiled TIFF, NPY, Zarr, and tiled-raster PM conversion. Applications that only need ANN/SEG/SR and GeoJSON conversion can disable default features to avoid those raster dependencies.

Applications provide an existing DICOM VL Whole Slide Microscopy instance as the source context. The crate preserves Study and Frame of Reference identity while assigning new Series and SOP Instance identities to derived objects.

GeoJSON to DICOM

QuPath classification labels are never guessed as clinical terminology. A bounded mapping profile must explicitly connect every label, measurement, and qualitative value to its DICOM coded meaning.

use std::fs;
use wsi_dicom_annotations::{
    DicomAnnotationContext, PathologyAnnotationSet, PathologyCoordinateSpace,
};

# fn main() -> Result<(), Box<dyn std::error::Error>> {
let source = DicomAnnotationContext::from_source("level-0-wsi.dcm")?;
let geojson = fs::read("qupath.geojson")?;
let mapping = fs::read("pathology-mapping-v1.json")?;
let annotations = PathologyAnnotationSet::from_json(
    &geojson,
    &mapping,
    &source,
    &source,
    PathologyCoordinateSpace::Level0Pixels,
    false,
)?;
annotations.to_ann()?.write_ann("annotations.dcm")?;
# Ok(())
# }

Polygon holes and mask-style regions belong in SEG rather than ANN. Numeric measurements and coded evaluations can be retained in SR, including SR that references the exact SEG generated from the same profiled feature set.

Scope

This crate owns DICOM interchange, terminology primitives, annotation schemes, tracking identity, and profiled external-data conversion. It deliberately does not contain a viewer, renderer, editing history, workspace persistence, PACS or DICOMweb transport, clinical workflow claims, or collaborative review state.

dicom-viewer consumes this library for import and export. The separate wsi-annotation-interop project remains an independent file-level conformance harness and does not share the production implementation.

Dependency security note

Local Zarr support currently resolves lru 0.16.4 through zarrs 0.23.14. RUSTSEC-2026-0253 requires a key with a panicking Drop implementation and unwind recovery; this dependency path uses only StoreKey(String) and ChunkIndices(Vec<u64>), whose drops cannot panic. The repository records this reachability decision explicitly, and dicom-viewer additionally applies the upstream source-level backport. Remove the exception when a compatible zarrs release permits lru >= 0.18.2.