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mpReview Development of a streamlined Slicer module for manual image annotation

Key Investigators

Project Description

The 3DSlicer module mpReview (part of the SlicerProstate extension) was previously developed to assist with manual annotation of the prostate and other related anatomical regions. In previous project weeks, we have streamlined the extension here and updated the module to use the latest SegmentEditor, and incorporated the use of Google Cloud Platform here.

However, there are improvements that can be made in terms of functionality. For instance, we would like to allow the user to access multiple types of servers, and perform annotation of body parts other than the prostate.

In this project week we’ll focus on using a JSON file as input, which will allow users to customize the module to their annotation needs. Our goal will be to streamline the user’s interaction with the module, allowing them to annotate large datasets efficiently and quickly using both the cloud (e.g. GCP and Kaapana) or a local DICOM database.

Objective

  1. Discuss the current multiple_server branch of the module.

  2. Brainstorm the JSON format specification necessary for streamlining the annotation workflow. Generate examples of JSON files for different use cases: local Slicer DICOM database, Google Cloud Platform, Kaapana, etc.

  3. Define the steps that are needed to accomplish the changes.

Approach and Plan

  1. We will discuss the state of the current branch, and identify the needs of users.
  2. After talking to researchers and clinicians and their annotation needs/concerns, we will develop JSON format specifications for a variety of use cases.

Progress and Next Steps

  1. We have started discussing the shortcomings of the current module.
  2. We have started to draft possible JSON file specifications.

Illustrations

Current screenshot of the module

image

Background and References

We have worked on this during multiple project weeks, PW35 and PW37. The code from PW37 is available here.