# Towards more precise automatic analysis: a comprehensive survey of deep learning-based multi-organ segmentation

arXiv: https://arxiv.org/abs/2303.00232 · HTML: https://mlsanity.com/paper/2303.00232/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 94 of its 217 references that are in the map.
- First posted on arXiv 1 Mar 2023.

## Builds on (most cited first, 30 of 94)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Densely Connected Convolutional Networks](https://mlsanity.com/paper/1608.06993/) (2016)
- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [Feature Pyramid Networks for Object Detection](https://mlsanity.com/paper/1612.03144/) (2016)
- [Fully Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1411.4038/) (2014)
- [DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs](https://mlsanity.com/paper/1606.00915/) (2016)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [Deformable Convolutional Networks](https://mlsanity.com/paper/1703.06211/) (2017)
- [Attention U-Net: Learning Where to Look for the Pancreas](https://mlsanity.com/paper/1804.03999/) (2018)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Generalised Dice overlap as a deep learning loss function for highly unbalanced segmentations](https://mlsanity.com/paper/1707.03237/) (2017)
- [The Liver Tumor Segmentation Benchmark (LiTS)](https://mlsanity.com/paper/1901.04056/) (2019)
- [A large annotated medical image dataset for the development and evaluation of segmentation algorithms](https://mlsanity.com/paper/1902.09063/) (2019)
- [Medical Transformer: Gated Axial-Attention for Medical Image Segmentation](https://mlsanity.com/paper/2102.10662/) (2021)
- [CHAOS Challenge -- Combined (CT-MR) Healthy Abdominal Organ Segmentation](https://mlsanity.com/paper/2001.06535/) (2020)
- [Med3D: Transfer Learning for 3D Medical Image Analysis](https://mlsanity.com/paper/1904.00625/) (2019)
- [Embracing Imperfect Datasets: A Review of Deep Learning Solutions for Medical Image Segmentation](https://mlsanity.com/paper/1908.10454/) (2019)
- [TransFuse: Fusing Transformers and CNNs for Medical Image Segmentation](https://mlsanity.com/paper/2102.08005/) (2021)
- [Tversky loss function for image segmentation using 3D fully convolutional deep networks](https://mlsanity.com/paper/1706.05721/) (2017)
- [CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.03024/) (2021)
- [AbdomenCT-1K: Is Abdominal Organ Segmentation A Solved Problem?](https://mlsanity.com/paper/2010.14808/) (2020)
- [A survey of loss functions for semantic segmentation](https://mlsanity.com/paper/2006.14822/) (2020)
- [UCTransNet: Rethinking the Skip Connections in U-Net from a Channel-wise Perspective with Transformer](https://mlsanity.com/paper/2109.04335/) (2021)
- [A Novel Focal Tversky loss function with improved Attention U-Net for lesion segmentation](https://mlsanity.com/paper/1810.07842/) (2018)

## Built on by (most cited first, 3 of 3)

- [Deep Mutual Learning among Partially Labeled Datasets for Multi-Organ Segmentation](https://mlsanity.com/paper/2407.12611/) (2024)
- [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)
- [Leveraging Transfer Learning with Class-Specific Decoders for Laparoscopic Segmentation](https://mlsanity.com/paper/2607.29509/) (2026)

## Abstract (arXiv)

Accurate segmentation of multiple organs of the head, neck, chest, and abdomen from medical images is an essential step in computer-aided diagnosis, surgical navigation, and radiation therapy. In the past few years, with a data-driven feature extraction approach and end-to-end training, automatic deep learning-based multi-organ segmentation method has far outperformed traditional methods and become a new research topic. This review systematically summarizes the latest research in this field. For the first time, from the perspective of full and imperfect annotation, we comprehensively compile 161 studies on deep learning-based multi-organ segmentation in multiple regions such as the head and neck, chest, and abdomen, containing a total of 214 related references. The method based on full annotation summarizes the existing methods from four aspects: network architecture, network dimension, network dedicated modules, and network loss function. The method based on imperfect annotation summarizes the existing methods from two aspects: weak annotation-based methods and semi annotation-based methods. We also summarize frequently used datasets for multi-organ segmentation and discuss new challenges and new research trends in this field.