Annotation Automation Ideas

[PaulHax]

Annotation Automation Ideas

Report Generation Post Process for Analyst

• Iterate over multiple scans with one call to the script.
• Additional computed columns in CSV, like ROI volume.

Annotation Pre Process for Annotators

• Generate ROIs given scan(s)
• Generate RECIST ruler measurements given ROIs

Annotation Linting During Annotation for Annotators

• In Volview check annotations match expectations and if not show helpful messages. Example: There are 2 unconnected ROIs with the same name.

Utopia Story

A north-star workflow motivating the feature requests above. Proprietary
pieces (🏭) are out of scope but mark where girder_volview should expose
extension points (🔌). ✅ = works today. 🚧 = in progress.

Personas: Admin (sets up collections and plugins), Annotator (reviews/edits in VolView),
Analyst (generates reports).

1. Admin imports a collection of scans into Girder. ✅
2. Admin generates initial annotations.
   • Runs a Slicer CLI job over the collection that writes a
     session.volview.zip per scan (segmentation labelmap + named rulers). 🔌
     Seam: a Slicer-CLI-job → session bridge built on the Session Builder library.
   • The model behind the job is custom/proprietary (e.g. in-house
     segmentation). 🏭
3. Annotator reviews and edits in VolView. ✅ (open/edit/save roundtrip)
   • If the Admin skipped step 2, the Annotator runs the annotation job
     from inside VolView. 🚧 (jobs-in-VolView feature)
   • On save, validation rules run and show helpful messages. 🔌🏭
     Seam: girder_volview exposes a save-time hook (🔌); rules are
     collection-specific (🏭).
4. Analyst generates a report.
   • Points a script, or a GUI at the collection's root Girder folder and gets CSV/JSON
     across all scans (LD/SAD lengths, ROI volume, warnings). 🔌
     Seam: fold the reporting utilities into the girder_volview Python library.
   • Built on the Session Builder library (session_builder/). ✅

Proprietary Extension Plugin

The 🏭 pieces live in a private Girder plugin installed alongside girder_volview.
It binds to girder_volview's events and imports the Session Builder library, so
maintainers owe stable seams, not knowledge of the proprietary code.

Once girder_volview fires the hooks (🔌), the private plugin binds to them;
report logic imports the library or adds its own REST endpoints; the
segmentation model ships as a Slicer CLI Docker image (no plugin code needed).