Slicer Cochlea

This is a 3D Slicer plugin that uses elastix toolbox for Multi-modal cochlea Images registration, segmentation and analysis. The elastix parameter files can be found here

Automatic Cochlea Registration and Fusion

Automatic Cochlea Image Segmentation and Analysis

This is a 3D Slicer plugin that uses elastix toolbox for Multi-modal cochlea Images registration, segmentation and analysis. The elastix parameters file can be found here

Tested on

• Slicer 5.6, Windows 10 and Ubuntu 20.04

This project contains three modules:

1. Cochlea image registration and fusion.
2. Cochlea image segmentation and analysis.
3. VisSimCommon for common functions.

How to use:

• In case you are new to 3D Slicer check my Slicer tutorials (notice that there maybe small difference between different versions):
  • 3D Slicer installation.
  • 3D Slicer introduction.
• See the documentation
• See the video tutorials for cochlea registration and fusion and cochlea segmentation and analysis

Publications:

Please cite our papers:

• Al-Dhamari I et al. (2023) Automatic Cochlea Multimodal 3D Image Segmentation And Analysis Using Atlas-model-based Method, Cochlear Implants International, DOI: 10.1080/14670100.2023.2274199. Link
• Al-Dhamari I, Helal R, Morozova O, Abdelaziz T, Jacob R, et al. (2022) Automatic intra-subject registration and fusion of multimodal cochlea 3D clinical images. PLOS ONE 17(3): e0264449. https://doi.org/10.1371/journal.pone.0264449. Link
• Ibraheem Al-Dhamari, Sabine Bauer, Dietrich Paulus, Roland Jacob, (2018), Automatic Cochlea Multi-modal Images Segmentation Using Adaptive Stochastic Gradient Descent. In: CI2018 DC Emerging Issues in Cochlear Implantation, Washington DC, USA.
• Ibraheem Al-Dhamari, Sabine Bauer, Dietrich Paulus, Friedrich Lisseck and Roland Jacob, (2017): ACIR: automatic cochlea image registration. In: Proceedings SPIE Medical Imaging 2017: Image Processing;. SPIE. Bd. 10133. S. 10133p1-10133p5. link

Notes:

• For general 3D Slicer questions, please use Slicer forum, many experts will be able to help you there.
• For Slicer cochlea related questions, comemnts, or feedback, please use github discussion section.
• For Slicer cochlea related bugs, please open a new issue if needed. Please mention your operating system, slicer version, and the error message you see in python interactor.
• For sharing private information, dataset, a future project proposal or cooperation, please use the email, use SlicerCochlea in the subject.
• It would be nice to share your anonymised cochlea dataset.
• It would be nice to contribute to this repository!

License

Copyright 2019, Dr. Ibraheem AL-Dhamari.

Licensed under the Apache License, Version 2.0.