# 3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation

arXiv: https://arxiv.org/abs/1606.06650 · HTML: https://mlsanity.com/paper/1606.06650/

## Key facts

- Cited by 1,476 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 21 Jun 2016.

## Built on by (most cited first, 30 of 1476)

- [Video Diffusion Models](https://mlsanity.com/paper/2204.03458/) (2022)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [Diffusion Models in Vision: A Survey](https://mlsanity.com/paper/2209.04747/) (2022)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [VoxPoser: Composable 3D Value Maps for Robotic Manipulation with Language Models](https://mlsanity.com/paper/2307.05973/) (2023)
- [ModelScope Text-to-Video Technical Report](https://mlsanity.com/paper/2308.06571/) (2023)
- [3D Shape Generation and Completion through Point-Voxel Diffusion](https://mlsanity.com/paper/2104.03670/) (2021)
- [Medical SAM Adapter: Adapting Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.12620/) (2023)
- [Learning Interactive Real-World Simulators](https://mlsanity.com/paper/2310.06114/) (2023)
- [Lumiere: A Space-Time Diffusion Model for Video Generation](https://mlsanity.com/paper/2401.12945/) (2024)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [MAGVIT: Masked Generative Video Transformer](https://mlsanity.com/paper/2212.05199/) (2022)
- [Medical Transformer: Gated Axial-Attention for Medical Image Segmentation](https://mlsanity.com/paper/2102.10662/) (2021)
- [Diffusion for World Modeling: Visual Details Matter in Atari](https://mlsanity.com/paper/2405.12399/) (2024)
- [VM-UNet: Vision Mamba UNet for Medical Image Segmentation](https://mlsanity.com/paper/2402.02491/) (2024)
- [Customized Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.13785/) (2023)
- [TransBTS: Multimodal Brain Tumor Segmentation Using Transformer](https://mlsanity.com/paper/2103.04430/) (2021)
- [Transformers in Medical Imaging: A Survey](https://mlsanity.com/paper/2201.09873/) (2022)
- [Medical Image Segmentation Review: The success of U-Net](https://mlsanity.com/paper/2211.14830/) (2022)
- [UNeXt: MLP-based Rapid Medical Image Segmentation Network](https://mlsanity.com/paper/2203.04967/) (2022)
- [Conditional Image-to-Video Generation with Latent Flow Diffusion Models](https://mlsanity.com/paper/2303.13744/) (2023)
- [U-KAN Makes Strong Backbone for Medical Image Segmentation and Generation](https://mlsanity.com/paper/2406.02918/) (2024)
- [MedNeXt: Transformer-driven Scaling of ConvNets for Medical Image Segmentation](https://mlsanity.com/paper/2303.09975/) (2023)
- [Zero-Shot Video Editing Using Off-The-Shelf Image Diffusion Models](https://mlsanity.com/paper/2303.17599/) (2023)
- [Diffusion-SDF: Text-to-Shape via Voxelized Diffusion](https://mlsanity.com/paper/2212.03293/) (2022)
- [FLamby: Datasets and Benchmarks for Cross-Silo Federated Learning in Realistic Healthcare Settings](https://mlsanity.com/paper/2210.04620/) (2022)
- [NeSF: Neural Semantic Fields for Generalizable Semantic Segmentation of 3D Scenes](https://mlsanity.com/paper/2111.13260/) (2021)
- [Bidirectional Copy-Paste for Semi-Supervised Medical Image Segmentation](https://mlsanity.com/paper/2305.00673/) (2023)
- [UNETR++: Delving into Efficient and Accurate 3D Medical Image Segmentation](https://mlsanity.com/paper/2212.04497/) (2022)

## Abstract (arXiv)

This paper introduces a network for volumetric segmentation that learns from sparsely annotated volumetric images. We outline two attractive use cases of this method: (1) In a semi-automated setup, the user annotates some slices in the volume to be segmented. The network learns from these sparse annotations and provides a dense 3D segmentation. (2) In a fully-automated setup, we assume that a representative, sparsely annotated training set exists. Trained on this data set, the network densely segments new volumetric images. The proposed network extends the previous u-net architecture from Ronneberger et al. by replacing all 2D operations with their 3D counterparts. The implementation performs on-the-fly elastic deformations for efficient data augmentation during training. It is trained end-to-end from scratch, i.e., no pre-trained network is required. We test the performance of the proposed method on a complex, highly variable 3D structure, the Xenopus kidney, and achieve good results for both use cases.