3D Slicer Uncertainty Visualizer

A 3D Slicer module for visualizing structure-wise uncertainty of vessels segmented by a deep learning model. The functionality involves adding, deleting, and viewing individual components based on their uncertainty values.

Installation and Setup

Prerequisites

• 3D Slicer installed on your system

Installation Steps

1. Clone the repository

   git clone https://github.com/your-username/3d-slicer-uncertainty-visualizer.git

2. Enable Developer Mode

   • Go to Slicer menu → Edit → Application Settings → Developer
   • Check "Enable Developer Mode"

3. Load the Extension

   • Navigate to Modules → Developer Tools → Extension Wizard
   • Click 'Select Extension'
   • Select the root folder of this GitHub repository
   • Select New as the module to load

4. Access the Module

   • Once the extension and module load successfully, go to Modules → Examples → New

Usage Instructions

Required Files

Before clicking "Generate Uncertainty Map", ensure you have loaded these 3 files as Volumes:

1. Uncertainty File

   • Rename this file following the pattern: *uncertainty_file* before loading
   • Load as Volume (use the float volume, not the int version)

2. Segmentation File

   • Rename this file following the pattern: *segmentation_file* before loading
   • Load as Volume

3. Image File

   • Load for visualization purposes

Important: Make sure no other files are loaded in Slicer that follow the above naming patterns.

Getting Started

1. Click the "Generate Uncertainty Map" button to begin working
2. The 'View' button for the 4th view (3D render) only works when the 4th view is in full screen mode

Development Notes

• Most of the code is located in New.py

Video Demonstrations

[YouTube] Our 3D Slicer plug-in video demo

[YouTube] 3D Slicer standard proof-reading tools' video demo