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Segment Editor clinical workflows

Key Investigators

Csaba Pinter (Queen's University, Canada)
~~Till Best~~
Nikos Makris (Brigham and Women's Hospital and Harvard Medical School, USA)
Filippo Cicali (Massachusetts General Hospital and Harvard Medical School, USA)
Tina Kapur (Brigham and Women’s Hospital and Harvard Medical School, USA)

Participating

Marco Nolden (DKFZ, Germany)
Attila Nagy (SZTE Medical School, Hungary)
Sharon Peled (Brigham and Women's Hospital and Harvard Medical School, USA)

Project Description

Objective

Segment Editor is the new manual and semi-automated image segmentation module in Slicer. It has powerful tools, but the learning curve can be steep for segmenting more complex cases.
The objective is to help researchers aiming to use Segment Edtitor use it for their specific use cases, and augment the training material based on the results

Approach and Plan

Each participating researcher brings a dataset, for which we'll attempt to develop an effective segmentation workflow
Add the developed workflows in the Slicer Segmentation Recipes page
- Publicly share dataset
- Create a tutorial page for the segmentation case including screenshots

Progress and Next Steps

Insula segmentation in MRI with Filippo Cicali and Nikos Makris
- Possible solution: Use Grow from seeds iteratively, then use scissors and masked paint to cut
- Consider speeding up segmentation by using a stylus instead of a mouse, and explore faster ways of slice navigation (3D mouse, webcam tracking, etc?)
Brachytherapy needle segmentation in MRI for training deep learning models
- Possible solution: Add "tube" mode from Markups to Models extension to Segment Editor, as an option to surface cut or a new effect in a new extension
- Deep learning training support: need cohort segmentation slicelet that allows configuring segment editor before segmenting first patient for simpler, less distracting user interface for easier usage and smoother and more reliable segmentation workflow
Minor help to multiple projects involving segmentation

Illustrations

Whole heart segmentation:

Spine phantom 3D printing:

Segment Editor in presentation in Casa África:

Background and References