# nnMamba: 3D Biomedical Image Segmentation, Classification and Landmark Detection with State Space Model

arXiv: https://arxiv.org/abs/2402.03526 · HTML: https://mlsanity.com/paper/2402.03526/

## Key facts

- Cited by 45 papers in the map (data through 14 Oct 2026).
- Builds on 41 of its 53 references that are in the map.
- First posted on arXiv 5 Feb 2024.

## Builds on (most cited first, 30 of 41)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Densely Connected Convolutional Networks](https://mlsanity.com/paper/1608.06993/) (2016)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Fully Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1411.4038/) (2014)
- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation](https://mlsanity.com/paper/1802.02611/) (2018)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [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)
- [Vision Mamba: Efficient Visual Representation Learning with Bidirectional State Space Model](https://mlsanity.com/paper/2401.09417/) (2024)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Stacked Hourglass Networks for Human Pose Estimation](https://mlsanity.com/paper/1603.06937/) (2016)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [Combining Recurrent, Convolutional, and Continuous-time Models with Linear State-Space Layers](https://mlsanity.com/paper/2110.13985/) (2021)
- [Network In Network](https://mlsanity.com/paper/1312.4400/) (2013)
- [Fully-Convolutional Siamese Networks for Object Tracking](https://mlsanity.com/paper/1606.09549/) (2016)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [ViTPose: Simple Vision Transformer Baselines for Human Pose Estimation](https://mlsanity.com/paper/2204.12484/) (2022)
- [U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation](https://mlsanity.com/paper/2401.04722/) (2024)
- [Deep Learning for Medical Image Analysis](https://mlsanity.com/paper/1708.08987/) (2017)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [SegMamba: Long-range Sequential Modeling Mamba For 3D Medical Image Segmentation](https://mlsanity.com/paper/2401.13560/) (2024)
- [CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.03024/) (2021)
- [Visual Saliency Based on Multiscale Deep Features](https://mlsanity.com/paper/1503.08663/) (2015)
- [nnFormer: Interleaved Transformer for Volumetric Segmentation](https://mlsanity.com/paper/2109.03201/) (2021)

## Built on by (most cited first, 30 of 45)

- [The Hidden Attention of Mamba Models](https://mlsanity.com/paper/2403.01590/) (2024)
- [ZigMa: A DiT-style Zigzag Mamba Diffusion Model](https://mlsanity.com/paper/2403.13802/) (2024)
- [Mamba-360: Survey of State Space Models as Transformer Alternative for Long Sequence Modelling: Methods, Applications, and Challenges](https://mlsanity.com/paper/2404.16112/) (2024)
- [State Space Model for New-Generation Network Alternative to Transformers: A Survey](https://mlsanity.com/paper/2404.09516/) (2024)
- [Vision Mamba: A Comprehensive Survey and Taxonomy](https://mlsanity.com/paper/2405.04404/) (2024)
- [A Survey on Visual Mamba](https://mlsanity.com/paper/2404.15956/) (2024)
- [VMRNN: Integrating Vision Mamba and LSTM for Efficient and Accurate Spatiotemporal Forecasting](https://mlsanity.com/paper/2403.16536/) (2024)
- [MambaLRP: Explaining Selective State Space Sequence Models](https://mlsanity.com/paper/2406.07592/) (2024)
- [Rethinking Scanning Strategies with Vision Mamba in Semantic Segmentation of Remote Sensing Imagery: An Experimental Study](https://mlsanity.com/paper/2405.08493/) (2024)
- [Res-VMamba: Fine-Grained Food Category Visual Classification Using Selective State Space Models with Deep Residual Learning](https://mlsanity.com/paper/2402.15761/) (2024)
- [Hybrid Mamba for Few-Shot Segmentation](https://mlsanity.com/paper/2409.19613/) (2024)
- [MambaMIR: An Arbitrary-Masked Mamba for Joint Medical Image Reconstruction and Uncertainty Estimation](https://mlsanity.com/paper/2402.18451/) (2024)
- [Mamba in Vision: A Comprehensive Survey of Techniques and Applications](https://mlsanity.com/paper/2410.03105/) (2024)
- [A Comprehensive Survey of Mamba Architectures for Medical Image Analysis: Classification, Segmentation, Restoration and Beyond](https://mlsanity.com/paper/2410.02362/) (2024)
- [CMViM: Contrastive Masked Vim Autoencoder for 3D Multi-modal Representation Learning for AD classification](https://mlsanity.com/paper/2403.16520/) (2024)
- [GroupMamba: Efficient Group-Based Visual State Space Model](https://mlsanity.com/paper/2407.13772/) (2024)
- [DenoMamba: A fused state-space model for low-dose CT denoising](https://mlsanity.com/paper/2409.13094/) (2024)
- [Deep Learning Techniques for Atmospheric Turbulence Removal: A Review](https://mlsanity.com/paper/2409.14587/) (2024)
- [ADAgent: LLM Agent for Alzheimer's Disease Analysis with Collaborative Coordinator](https://mlsanity.com/paper/2506.11150/) (2025)
- [FER-YOLO-Mamba: Facial Expression Detection and Classification Based on Selective State Space](https://mlsanity.com/paper/2405.01828/) (2024)
- [Diffuse-UDA: Addressing Unsupervised Domain Adaptation in Medical Image Segmentation with Appearance and Structure Aligned Diffusion Models](https://mlsanity.com/paper/2408.05985/) (2024)
- [VasTSD: Learning 3D Vascular Tree-state Space Diffusion Model for Angiography Synthesis](https://mlsanity.com/paper/2503.12758/) (2025)
- [MAMAT: 3D Mamba-Based Atmospheric Turbulence Removal and its Object Detection Capability](https://mlsanity.com/paper/2503.17700/) (2025)
- [Mamba-UIE: Enhancing Underwater Images with Physical Model Constraint](https://mlsanity.com/paper/2407.19248/) (2024)
- [TTT-Unet: Enhancing U-Net with Test-Time Training Layers for Biomedical Image Segmentation](https://mlsanity.com/paper/2409.11299/) (2024)
- [DH-Mamba: Exploring Dual-domain Hierarchical State Space Models for MRI Reconstruction](https://mlsanity.com/paper/2501.08163/) (2025)
- [nnLandmark: A Self-Configuring Method for 3D Medical Landmark Detection](https://mlsanity.com/paper/2504.06742/) (2025)
- [Technologies on Effectiveness and Efficiency: A Survey of State Spaces Models](https://mlsanity.com/paper/2503.11224/) (2025)
- [HWA-UNETR: Hierarchical Window Aggregate UNETR for 3D Multimodal Gastric Lesion Segmentation](https://mlsanity.com/paper/2505.10464/) (2025)
- [Uncertainty-aware Diffusion and Reinforcement Learning for Joint Plane Localization and Anomaly Diagnosis in 3D Ultrasound](https://mlsanity.com/paper/2506.23538/) (2025)

## Abstract (arXiv)

In the field of biomedical image analysis, the quest for architectures capable of effectively capturing long-range dependencies is paramount, especially when dealing with 3D image segmentation, classification, and landmark detection. Traditional Convolutional Neural Networks (CNNs) struggle with locality respective field, and Transformers have a heavy computational load when applied to high-dimensional medical images.In this paper, we introduce nnMamba, a novel architecture that integrates the strengths of CNNs and the advanced long-range modeling capabilities of State Space Sequence Models (SSMs). Specifically, we propose the Mamba-In-Convolution with Channel-Spatial Siamese learning (MICCSS) block to model the long-range relationship of the voxels. For the dense prediction and classification tasks, we also design the channel-scaling and channel-sequential learning methods. Extensive experiments on 6 datasets demonstrate nnMamba's superiority over state-of-the-art methods in a suite of challenging tasks, including 3D image segmentation, classification, and landmark detection. nnMamba emerges as a robust solution, offering both the local representation ability of CNNs and the efficient global context processing of SSMs, setting a new standard for long-range dependency modeling in medical image analysis. Code is available at https://github.com/lhaof/nnMamba