2012 Project Week:QIN-SAM

From NAMIC Wiki
Jump to: navigation, search
Home < 2012 Project Week:QIN-SAM

Key Investigators

  • BWH: Andrey Fedorov, Nicole Aucoin, Fiona Fennessy
  • Isomics: Steve Pieper
  • MGH: Jayashree Kalpathy-Cramer
  • Radnostics: Anthony Blumfield


Our longer-term goal is to be able to store annotations created in Slicer in a format that

  • facilitates sharing annotations across groups
  • supported by tools other than Slicer
  • search and query friendly
  • supports use cases provided by the clinical research community (and specifically those provided by the QIN community QIN use cases)
  • ideally supports convenient and established API for interacting with the stored annotations

Our goal at this meeting is to discuss the architecture and work on implementing support of Annotation&Markup in 3D Slicer, as part of supporting the annotation markup needs of the NCI QIN project.

Approach, Plan

The project is summarized in detail here: Projects:QIN:3D_Slicer_Annotation_Image_Markup. During the meeting, we will discuss the existing and desired Slicer capabilities, use cases, and will start working on the implementation and module design, according to the plan outlined here Projects:QIN:3D_Slicer_Annotation_Image_Markup:Design_and_Implementation.


  • We had a discussion of DICOM RT, SR and needs of this project (2012_Winter_Project_Week_DICOM_RT_Breakout). There is a common need to provide (1) explicit connection between annotation/markup elements and images; (2) connection between the slices of the volume and DICOM image UIDs. BWH will work on this as part of QIN AIM project.
  • Use cases were discussed in more depth with the Jayashree (MGH), and made progress with implementation plans details.
  • Several annotation templates used at MGH were identified for testing purposes.
  • The module providing structured annotation and markup functionality in Slicer will be called "Reporting Module", source code available on github: https://github.com/fedorov/Reporting
  • Annotation (text) / markup (visual elements) serialization will be most likely done using AIM, since we were not able to identify manageable APIs and reference tools to use DICOM SR. We may need to use intermediate format ("AIM-light"?) for serialization, since most up-to-date AIM API is Java-based.
  • We identified new projects interested in the structured reporting functionality, compatible with clinical systems (Anthony).

See more details for this project on the main project page: Projects:QIN:3D_Slicer_Annotation_Image_Markup.

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as an extension of 3D Slicer 4