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Interactive Segmentation Using the SegmentEditor

Key Investigators

  • Houssem Gueziri (MNI)

Project Description

Fast Delineation by Random Walker (FastDRaW) is a graph-based interactive segmentation approach implemented in Python. This project aims at implementing a plugin in the SegmentEditor to perform FastDRaW in 3D Slicer.

Objective

  1. Learn how to use the SegmentEditor to develop plugins
  2. Integrate python-based code to Slicer

Approach and Plan

  1. Develop a toy example segmentation using the SegmentEditor
  2. Starts from the Grow from seeds plugin to adapt to FastDRaW

Progress and Next Steps

  1. Added FastDRaWEffect extension to the SegmentEditor
  2. Added merged python implementation of fastDRaW
  3. Get segmentation from numpy array and convert it to vtkImageData to display preview
  4. Add GUI to set parameters (beta parameter)
  5. Add GUI to select active label

TODO

  1. Currently, the segmentation does not update when a non-target label is beeing modified
  2. Updating the graph costs when the beta parameter is modified (building the graph is time consuming, maybe create a dedicated button to rebuild the graph when beta changes?)
  3. Clean code and group source files in single folder
  4. Learn how to make downladable extension

Illustrations

Screenshot Screenshot2

Background and References