# Automatic Segmentation of Organs-at-Risk from Head-and-Neck CT using Separable Convolutional Neural Network with Hard-Region-Weighted Loss

arXiv: https://arxiv.org/abs/2102.01897 · HTML: https://mlsanity.com/paper/2102.01897/

## Key facts

- Cited by 9 papers in the map (data through 14 Oct 2026).
- Builds on 26 of its 53 references that are in the map.
- First posted on arXiv 3 Feb 2021.

## Builds on (most cited first, 26 of 26)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Fully Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1411.4038/) (2014)
- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles](https://mlsanity.com/paper/1612.01474/) (2016)
- [What Uncertainties Do We Need in Bayesian Deep Learning for Computer Vision?](https://mlsanity.com/paper/1703.04977/) (2017)
- [Xception: Deep Learning with Depthwise Separable Convolutions](https://mlsanity.com/paper/1610.02357/) (2016)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Instance Normalization: The Missing Ingredient for Fast Stylization](https://mlsanity.com/paper/1607.08022/) (2016)
- [Aleatoric uncertainty estimation with test-time augmentation for medical image segmentation with convolutional neural networks](https://mlsanity.com/paper/1807.07356/) (2018)
- [CE-Net: Context Encoder Network for 2D Medical Image Segmentation](https://mlsanity.com/paper/1903.02740/) (2019)
- [Bayesian Deep Convolutional Encoder-Decoder Networks for Surrogate Modeling and Uncertainty Quantification](https://mlsanity.com/paper/1801.06879/) (2018)
- [Exploring Uncertainty Measures in Deep Networks for Multiple Sclerosis Lesion Detection and Segmentation](https://mlsanity.com/paper/1808.01200/) (2018)
- [Reducing the Hausdorff Distance in Medical Image Segmentation with Convolutional Neural Networks](https://mlsanity.com/paper/1904.10030/) (2019)
- [Interactive Medical Image Segmentation using Deep Learning with Image-specific Fine-tuning](https://mlsanity.com/paper/1710.04043/) (2017)
- [Deep learning to achieve clinically applicable segmentation of head and neck anatomy for radiotherapy](https://mlsanity.com/paper/1809.04430/) (2018)
- [AnatomyNet: Deep Learning for Fast and Fully Automated Whole-volume Segmentation of Head and Neck Anatomy](https://mlsanity.com/paper/1808.05238/) (2018)
- [3D Segmentation with Exponential Logarithmic Loss for Highly Unbalanced Object Sizes](https://mlsanity.com/paper/1809.00076/) (2018)
- [Closing the Gap between Deep and Conventional Image Registration using Probabilistic Dense Displacement Networks](https://mlsanity.com/paper/1907.10931/) (2019)
- [Automatic Brain Tumor Segmentation using Cascaded Anisotropic Convolutional Neural Networks](https://mlsanity.com/paper/1709.00382/) (2017)
- [FocusNet: Imbalanced Large and Small Organ Segmentation with an End-to-End Deep Neural Network for Head and Neck CT Images](https://mlsanity.com/paper/1907.12056/) (2019)
- [Improving Computer-aided Detection using Convolutional Neural Networks and Random View Aggregation](https://mlsanity.com/paper/1505.03046/) (2015)
- [Inherent Brain Segmentation Quality Control from Fully ConvNet Monte Carlo Sampling](https://mlsanity.com/paper/1804.07046/) (2018)
- [Uncertainty-Guided Efficient Interactive Refinement of Fetal Brain Segmentation from Stacks of MRI Slices](https://mlsanity.com/paper/2007.00833/) (2020)

## Built on by (most cited first, 9 of 9)

- [SegRap2023: A Benchmark of Organs-at-Risk and Gross Tumor Volume Segmentation for Radiotherapy Planning of Nasopharyngeal Carcinoma](https://mlsanity.com/paper/2312.09576/) (2023)
- [SegReg: Segmenting OARs by Registering MR Images and CT Annotations](https://mlsanity.com/paper/2311.06956/) (2023)
- [Towards more precise automatic analysis: a comprehensive survey of deep learning-based multi-organ segmentation](https://mlsanity.com/paper/2303.00232/) (2023)
- [One-shot Weakly-Supervised Segmentation in Medical Images](https://mlsanity.com/paper/2111.10773/) (2021)
- [HMRNet: High and Multi-Resolution Network with Bidirectional Feature Calibration for Brain Structure Segmentation in Radiotherapy](https://mlsanity.com/paper/2206.02959/) (2022)
- [Deep-learning Segmentation of Small Volumes in CT images for Radiotherapy Treatment Planning](https://mlsanity.com/paper/2404.04202/) (2024)
- [MFM-DA: Instance-Aware Adaptor and Hierarchical Alignment for Efficient Domain Adaptation in Medical Foundation Models](https://mlsanity.com/paper/2503.00802/) (2025)
- [MOSAIC: A Multi-View 2.5D Organ Slice Selector with Cross-Attentional Reasoning for Anatomically-Aware CT Localization in Medical Organ Segmentation](https://mlsanity.com/paper/2505.10672/) (2025)
- [Advances in Medical Image Segmentation: A Comprehensive Survey with a Focus on Lumbar Spine Applications](https://mlsanity.com/paper/2510.03318/) (2025)

## Abstract (arXiv)

Nasopharyngeal Carcinoma (NPC) is a leading form of Head-and-Neck (HAN) cancer in the Arctic, China, Southeast Asia, and the Middle East/North Africa. Accurate segmentation of Organs-at-Risk (OAR) from Computed Tomography (CT) images with uncertainty information is critical for effective planning of radiation therapy for NPC treatment. Despite the stateof-the-art performance achieved by Convolutional Neural Networks (CNNs) for automatic segmentation of OARs, existing methods do not provide uncertainty estimation of the segmentation results for treatment planning, and their accuracy is still limited by several factors, including the low contrast of soft tissues in CT, highly imbalanced sizes of OARs and large inter-slice spacing. To address these problems, we propose a novel framework for accurate OAR segmentation with reliable uncertainty estimation. First, we propose a Segmental Linear Function (SLF) to transform the intensity of CT images to make multiple organs more distinguishable than existing methods based on a simple window width/level that often gives a better visibility of one organ while hiding the others. Second, to deal with the large inter-slice spacing, we introduce a novel 2.5D network (named as 3D-SepNet) specially designed for dealing with clinic HAN CT scans with anisotropic spacing. Thirdly, existing hardness-aware loss function often deal with class-level hardness, but our proposed attention to hard voxels (ATH) uses a voxel-level hardness strategy, which is more suitable to dealing with some hard regions despite that its corresponding class may be easy. Our code is now available at https://github.com/HiLab-git/SepNet.