Refine pathology workspace and extract the headless annotation CLI

.cargo/config.toml

@@ -0,0 +1,2 @@
+[target.x86_64-pc-windows-msvc]
+rustflags = ["-C", "target-feature=+crt-static"]

.github/workflows/ci.yml

@@ -28,14 +28,6 @@ jobs:
           path: dicom-viewer
           persist-credentials: false
 
-      - name: Checkout wsi-dicom-annotations
-        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
-        with:
-          repository: frames-sg/wsi-dicom-annotations
-          ref: a623e84405d9be6779e7065a71031228b20849a5
-          path: wsi-dicom-annotations
-          persist-credentials: false
-
       - name: Install Linux GUI dependencies
         if: runner.os == 'Linux'
         run: |
@@ -108,14 +100,6 @@ jobs:
           path: dicom-viewer
           persist-credentials: false
 
-      - name: Checkout wsi-dicom-annotations
-        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
-        with:
-          repository: frames-sg/wsi-dicom-annotations
-          ref: a623e84405d9be6779e7065a71031228b20849a5
-          path: wsi-dicom-annotations
-          persist-credentials: false
-
       - name: Install Rust
         uses: dtolnay/rust-toolchain@a75363d06101555fc97c6c7e1e65670b99104d98 # 1.96.1
 

.gitignore

@@ -2,3 +2,55 @@
 /.DS_Store
 *.profraw
 *.profdata
+
+# Local tools, credentials, and editor state
+.DS_Store
+.codex/
+.claude/
+.local-docs/
+.local-tools/
+.codex-security-*/
+reasonix.toml
+.env
+.env.*
+!.env.example
+!.env.sample
+*.key
+*.pem
+*.p12
+*.pfx
+.vscode/
+.idea/
+*.swp
+
+# Local dependencies, build outputs, and caches
+node_modules/
+.venv*/
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.ruff_cache/
+/dist/
+/coverage/
+lcov*.info
+*.log
+
+# Private writing and execution plans; maintained outside the software repos
+/manuscript/
+/grant/
+/paper/
+/papers/
+/uscap/
+/docs/manuscript/
+/docs/USCAP*
+/docs/papers/
+/docs/benchmarks/paper/
+/docs/plans/
+/docs/workplans/
+/docs/refactor/
+/docs/superpowers/
+/MIGRATION.md
+/migration.md
+*.docx
+*.pptx
+*.pdf

Cargo.toml

@@ -5,7 +5,7 @@ members = [
     "crates/dicom-viewer-core",
     "crates/metal-wgpu-interop",
 ]
-exclude = ["vendor/lru", "vendor/wayland-scanner"]
+exclude = ["vendor/epaint", "vendor/lru", "vendor/wayland-scanner"]
 
 [workspace.package]
 edition = "2021"
@@ -16,10 +16,7 @@ repository = "https://github.com/frames-sg/dicom-viewer"
 [workspace.dependencies]
 dicom-core = "0.9"
 dicom-dictionary-std = "0.9"
-dicom-encoding = "0.9"
 dicom-object = "0.9"
-dicom-parser = "0.9"
-dicom-transfer-syntax-registry = { version = "0.9", default-features = false }
 eframe = { version = "0.34.2", default-features = false, features = [
     "accesskit",
     "default_fonts",
@@ -43,17 +40,18 @@ serde = { version = "1", features = ["derive", "rc"] }
 wsi-rs = { version = "0.6.0", git = "https://github.com/frames-sg/wsi-rs.git", rev = "b940ea94f3290e54ca2c5f87823109538709c59d" }
 tempfile = "3"
 thiserror = "2"
+tiff = "0.11.3"
 lcms2 = { version = "6.1.1", features = ["static"] }
 sha2 = "0.10"
 uuid = { version = "1", features = ["serde", "v4"] }
 geo = { version = "0.33.1", default-features = false }
 rstar = "0.12.2"
-peak_alloc = "0.3"
-wsi-dicom-annotations = { version = "=0.1.1", path = "../wsi-dicom-annotations" }
+wsi-dicom-annotations = { version = "=0.1.2", git = "https://github.com/frames-sg/wsi-dicom-annotations.git", rev = "71851b4a0c286fa9b57326e426962bf1a63a781e" }
 
-# Temporary security patches for advisories without compatible upstream
-# releases. See each vendored crate's SECURITY-PATCH.md for removal criteria.
+# Dependency patches and the Windows font backend; see SUPPLY_CHAIN.md.
+# Security-patched crates retain their SECURITY-PATCH.md removal criteria.
 [patch.crates-io]
+epaint = { path = "vendor/epaint" }
 lru = { path = "vendor/lru" }
 wayland-scanner = { path = "vendor/wayland-scanner" }
 

README.md

@@ -2,19 +2,14 @@
 
 Lightweight desktop viewer for local whole-slide image files through `wsi-rs`.
 
-This application is for research use only. It is not a medical device and is
-not intended for diagnosis, treatment decisions, or other clinical use. Use
-only research inputs that contain no patient data; the viewer does not perform
-de-identification or validate that an input is free of identifying metadata.
-
 The app is intended for checking `wsi-dicom` output locally and for verifying
 other wsi-rs-supported WSI inputs. It does not upload files or use DICOMweb.
 Its facts panel reads only the technical WSI tags documented below; local file
 paths can still be visible in the UI and in screenshots.
 
 See [Architecture](docs/ARCHITECTURE.md) for ownership, scheduling, cache, and
 Metal interoperability invariants, the [pathology annotation
-workflow](docs/ANNOTATION_WORKFLOW.md), and the [research release
+workflow](docs/ANNOTATION_WORKFLOW.md), and the [release
 checklist](docs/RELEASE.md) for distribution gates.
 
 ## Build
@@ -27,6 +22,15 @@ complete revisions, so no sibling codec checkout is required.
 cargo run -p dicom-viewer
 ```
 
+Build the standalone Windows GUI executable on an x86-64 Windows host with:
+
+```powershell
+cargo build -p dicom-viewer --bin dicom-viewer --release --locked
+```
+
+The Windows build statically links the MSVC runtime, so the resulting
+`target\release\dicom-viewer.exe` requires no application-specific sidecar DLLs.
+
 wgpu is the only presentation backend on every platform. On macOS, ordinary
 builds automatically enable `wsi-rs` Metal decoding and use the renderer's
 exact Metal device; resident RGB tiles are converted to RGBA by a wgpu compute
@@ -81,7 +85,7 @@ space, wsi-rs source caches, or GPU driver overhead.
 DICOM inspection rejects metadata beyond explicit resource limits before the
 eager object parser runs: 1 MiB of file-meta data, 16 MiB per primitive value,
 128 MiB of cumulative primitive values, two million metadata tokens, and 64
-nested sequences. These are research-viewer safety limits rather than DICOM
+nested sequences. These are viewer safety limits rather than DICOM
 conformance claims.
 
 ## Pathology annotation workspace
@@ -129,10 +133,20 @@ contract](docs/FRAMES_PATHOLOGY_GEOJSON_V1.md), [tumor-mask compatibility
 adapter](docs/TUMOR_MASK_COMPATIBILITY.md), and [workspace storage/privacy
 notes](docs/WORKSPACE_STORAGE.md).
 
+### Annotation dependency source
+
+Annotations 0.1.2 is pinned to immutable Git revision
+`71851b4a0c286fa9b57326e426962bf1a63a781e` in `frames-sg/wsi-dicom-annotations`.
+That revision owns the shared metadata reader and headless CLI. CI checks out only
+the viewer; Cargo resolves the owner without a sibling directory or local overlay.
+The dependency remains versioned and locked. A later registry migration requires
+publication of the matching API and a reviewed lockfile refresh.
+
 ### Headless annotation interoperability probe
 
-`annotation_probe` is a thin CLI over the separately versioned
-`wsi-dicom-annotations` library. It exposes ANN/SEG parsing and rewriting plus
+`annotation_probe` is maintained in the `wsi-dicom-annotations` repository as the
+`wsi-annotation-probe` package. Build it there with
+`cargo build -p wsi-annotation-probe --bin annotation_probe --locked`. It exposes ANN/SEG parsing and rewriting plus
 Rust-owned GeoJSON and raster conversion without the GUI. It writes one
 schema-versioned JSON object to stdout; warnings and human-readable failures go
 to stderr.
@@ -207,8 +221,6 @@ Dual-licensed under either [MIT](LICENSE-MIT) or
 
 ## Current Scope
 
-- Research-use-only operation with non-patient inputs; no clinical claims or
-  de-identification workflow.
 - Desktop-only `egui/eframe` app with a unified wgpu renderer.
 - Open one wsi-rs-supported WSI file or a folder of DICOM instances.
 - View WSI levels as tiled RGB/RGBA pixels through `wsi-rs`.