Documentation/Nightly/Modules/DeepInfer

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Introduction and Acknowledgements

Extension: DeepInfer
Acknowledgments: This work is funded by NIH Grant No.P41EB015898, Natural Sciences andEngineering Research Council (NSERC) of Canada and the Canadian Institutes of Health Research (CIHR).
Authors: Alireza Mehrtash(SPL), Mehran Pesteie ()
Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email>
webite: DeepInfer Website
License: Slicer License


Surgical Planning Laboratory (SPL)  

Module Description

Deepinfer-256.png
DeepInfer is an Open-Source Deep Learning Deployment Toolkit for medical imaging and Image-Guided Therapy. With DeepInfer 3D Slicer users can deploy trained deep learning and machine learning models in their workflow. Also, DeepInfer allows machine learning experts to package, ship, and deploy their models, thereby additionally allowing clinical researchers and biomedical engineers to use task-specific deep models, without the need for further software development and configuration.

Setup Guide

In order to use DeepInfer, Docker is required to be installed and configured properly.

Windows

Docker for Windows requires Windows 10 Pro (64bit) and Microsoft Hyper-V. You also need to enable virtualization in BIOS settings.

Mac OS X

Ubuntu

Tutorials

Panels and their use

Deployed Models

Prostate Segmentation in Targeted MRI-Guided Biopsy

This model is trained for the task of rough delineation of the prostate gland that is a necessary step in MRI-guided targeted biopsy. The deployed model is trained on transaxial T2-weighted MRIs of the prostate (without endorectal coil on a 3T MRI machine) collected during MR-guided prostate biopsy procedures. The network based on a customized variant of the U-Net architecture. The network is trained on N = 224 patients on a total number of 26250 2D slices of prostate images and achieved 76.25% accuracy on N = 57 validation patients (2184 2D slices).

Prostate-deepinfer.png

Citing DeepInfer

To acknowledge DeepInfer and 3D Slicer, please cite the please cite the DeepInfer web site and following publications when publishing work that uses or incorporates DeepInfer and 3D Slicer:

Information for Developers