3D Slicer Extension Tutorials

Learn how to create an extension for 3D Slicer: extract volumes and slices, run ML models, edit segmentations, and much more.

3 Parts

24m Read

#1 Loading Volumes and Creating Segments

10 min Read

Get started with creating an extension, loading volumes, and creating segments using an embedded SegmentEditor widget.

Getting Started

Enable Developer Mode

The Extension Wizard

Developing our Module

The End Goal

The UI

The Widget

The Logic

Segmentation Node and the Segment Editor

The Widget (Again)

Conclusion

#2 Manipulating Segments With Python

10 min Read

Learn how to draw a segmentation mask on a slice with the click of a button.

The UI

The Widget

The Logic

Understanding Segment Updates

Drawing on Coronal or Saggital Slices

I see an ellipse

Conclusion

#3 Getting a segment via an API

4 min Read

Learn how to segment the loaded volume via an API running a ML model.

API Setup

The UI

The Widget

The Logic

Testing (Manually)

Conclusion

ML Inference on Backend vs Frontend

A comparison of ML inference speed and memory consumption across various batch sizes on both GPU and CPU.

05m Read

Drawing Images in React using Konva and extracting Image Arrays

Konva.js is a 2D Canvas Library for the web. We'll draw an image using Konva, extract the image array, and call an API to run an ML model on the image.

07m Read

ONNXRuntime Inference in a React App

Inferencing on an ONNX model in a React App using ONNXRuntime Web.

08m Read