3D MRI brain tumor segmentation using autoencoder regularization
@inproceedings{Myronenko20183DMB, title={3D MRI brain tumor segmentation using autoencoder regularization}, author={Andriy Myronenko}, booktitle={BrainLes@MICCAI}, year={2018} }
Automated segmentation of brain tumors from 3D magnetic resonance images (MRIs) is necessary for the diagnosis, monitoring, and treatment planning of the disease. [] Key Method Due to a limited training dataset size, a variational auto-encoder branch is added to reconstruct the input image itself in order to regularize the shared decoder and impose additional constraints on its layers. The current approach won 1st place in the BraTS 2018 challenge.
570 Citations
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References
SHOWING 1-10 OF 22 REFERENCES
Learning Contextual and Attentive Information for Brain Tumor Segmentation
- Computer ScienceBrainLes@MICCAI
- 2018
This work designs multiple deep architectures of varied structures to learning contextual and attentive information, then ensemble the predictions of these models to obtain more robust segmentation results, and shows that the risk of overfitting in segmentation is reduced.
Automatic Brain Tumor Segmentation Using Cascaded Anisotropic Convolutional Neural Networks
- Computer ScienceBrainLes@MICCAI
- 2017
A cascade of fully convolutional neural networks is proposed to segment multi-modal Magnetic Resonance (MR) images with brain tumor into background and three hierarchical regions: whole tumor, tumor…
Ensembles of Densely-Connected CNNs with Label-Uncertainty for Brain Tumor Segmentation
- Computer ScienceBrainLes@MICCAI
- 2018
We introduce a new family of classifiers based on our previous DeepSCAN architecture, in which densely connected blocks of dilated convolutions are embedded in a shallow U-net-style structure of…
V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation
- Computer Science2016 Fourth International Conference on 3D Vision (3DV)
- 2016
This work proposes an approach to 3D image segmentation based on a volumetric, fully convolutional, neural network, trained end-to-end on MRI volumes depicting prostate, and learns to predict segmentation for the whole volume at once.
The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)
- Computer ScienceIEEE Transactions on Medical Imaging
- 2015
The set-up and results of the Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) organized in conjunction with the MICCAI 2012 and 2013 conferences are reported, finding that different algorithms worked best for different sub-regions, but that no single algorithm ranked in the top for all sub-Regions simultaneously.
Efficient multi‐scale 3D CNN with fully connected CRF for accurate brain lesion segmentation
- Computer ScienceMedical Image Anal.
- 2017
Ensembles of Multiple Models and Architectures for Robust Brain Tumour Segmentation
- Computer ScienceBrainLes@MICCAI
- 2017
This paper explores Ensembles of Multiple Models and Architectures (EMMA) for robust performance through aggregation of predictions from a wide range of methods to reduce the influence of the meta-parameters of individual models and the risk of overfitting the configuration to a particular database.
Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge
- MedicineArXiv
- 2018
This study assesses the state-of-the-art machine learning methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018, and investigates the challenge of identifying the best ML algorithms for each of these tasks.
U-Net: Convolutional Networks for Biomedical Image Segmentation
- Computer ScienceMICCAI
- 2015
It is shown that such a network can be trained end-to-end from very few images and outperforms the prior best method (a sliding-window convolutional network) on the ISBI challenge for segmentation of neuronal structures in electron microscopic stacks.
Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features
- MedicineScientific data
- 2017
This set of labels and features should enable direct utilization of the TCGA/TCIA glioma collections towards repeatable, reproducible and comparative quantitative studies leading to new predictive, prognostic, and diagnostic assessments, as well as performance evaluation of computer-aided segmentation methods.