# MA-SAM: Modality-agnostic SAM Adaptation for 3D Medical Image Segmentation

arXiv: https://arxiv.org/abs/2309.08842 · HTML: https://mlsanity.com/paper/2309.08842/

## Key facts

- Cited by 82 papers in the map (data through 14 Oct 2026).
- Builds on 49 of its 61 references that are in the map.
- First posted on arXiv 16 Sep 2023.

## Builds on (most cited first, 30 of 49)

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Parameter-Efficient Transfer Learning for NLP](https://mlsanity.com/paper/1902.00751/) (2019)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [Scaling Up Visual and Vision-Language Representation Learning With Noisy Text Supervision](https://mlsanity.com/paper/2102.05918/) (2021)
- [Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation](https://mlsanity.com/paper/1802.02611/) (2018)
- [Visual Prompt Tuning](https://mlsanity.com/paper/2203.12119/) (2022)
- [Conditional Prompt Learning for Vision-Language Models](https://mlsanity.com/paper/2203.05557/) (2022)
- [BitFit: Simple Parameter-efficient Fine-tuning for Transformer-based Masked Language-models](https://mlsanity.com/paper/2106.10199/) (2021)
- [Towards a Unified View of Parameter-Efficient Transfer Learning](https://mlsanity.com/paper/2110.04366/) (2021)
- [Florence: A New Foundation Model for Computer Vision](https://mlsanity.com/paper/2111.11432/) (2021)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [Segment Everything Everywhere All at Once](https://mlsanity.com/paper/2304.06718/) (2023)
- [Medical SAM Adapter: Adapting Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.12620/) (2023)
- [Self-Supervised Pre-Training of Swin Transformers for 3D Medical Image Analysis](https://mlsanity.com/paper/2111.14791/) (2021)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [Customized Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.13785/) (2023)
- [ST-Adapter: Parameter-Efficient Image-to-Video Transfer Learning](https://mlsanity.com/paper/2206.13559/) (2022)
- [nnFormer: Interleaved Transformer for Volumetric Segmentation](https://mlsanity.com/paper/2109.03201/) (2021)
- [Scaling Down to Scale Up: A Guide to Parameter-Efficient Fine-Tuning](https://mlsanity.com/paper/2303.15647/) (2023)
- [Segment Anything Model (SAM) for Digital Pathology: Assess Zero-shot Segmentation on Whole Slide Imaging](https://mlsanity.com/paper/2304.04155/) (2023)
- [FacT: Factor-Tuning for Lightweight Adaptation on Vision Transformer](https://mlsanity.com/paper/2212.03145/) (2022)
- [2018 Robotic Scene Segmentation Challenge](https://mlsanity.com/paper/2001.11190/) (2020)
- [MS-Net: Multi-Site Network for Improving Prostate Segmentation with Heterogeneous MRI Data](https://mlsanity.com/paper/2002.03366/) (2020)
- [SurgicalSAM: Efficient Class Promptable Surgical Instrument Segmentation](https://mlsanity.com/paper/2308.08746/) (2023)
- [Test-Time Adaptable Neural Networks for Robust Medical Image Segmentation](https://mlsanity.com/paper/2004.04668/) (2020)
- [3D UX-Net: A Large Kernel Volumetric ConvNet Modernizing Hierarchical Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2209.15076/) (2022)
- [SAM on Medical Images: A Comprehensive Study on Three Prompt Modes](https://mlsanity.com/paper/2305.00035/) (2023)

## Built on by (most cited first, 30 of 82)

- [SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images](https://mlsanity.com/paper/2310.15161/) (2023)
- [MedSAM2: Segment Anything in 3D Medical Images and Videos](https://mlsanity.com/paper/2504.03600/) (2025)
- [Foundation Model for Advancing Healthcare: Challenges, Opportunities, and Future Directions](https://mlsanity.com/paper/2404.03264/) (2024)
- [Open-Vocabulary SAM: Segment and Recognize Twenty-thousand Classes Interactively](https://mlsanity.com/paper/2401.02955/) (2024)
- [SA-Med2D-20M Dataset: Segment Anything in 2D Medical Imaging with 20 Million masks](https://mlsanity.com/paper/2311.11969/) (2023)
- [Domain Generalization for Medical Image Analysis: A Review](https://mlsanity.com/paper/2310.08598/) (2023)
- [Segment Anything in Medical Images and Videos: Benchmark and Deployment](https://mlsanity.com/paper/2408.03322/) (2024)
- [How to build the best medical image segmentation algorithm using foundation models: a comprehensive empirical study with Segment Anything Model](https://mlsanity.com/paper/2404.09957/) (2024)
- [DarkSAM: Fooling Segment Anything Model to Segment Nothing](https://mlsanity.com/paper/2409.17874/) (2024)
- [Foundation Models for Biomedical Image Segmentation: A Survey](https://mlsanity.com/paper/2401.07654/) (2024)
- [Forging Vision Foundation Models for Autonomous Driving: Challenges, Methodologies, and Opportunities](https://mlsanity.com/paper/2401.08045/) (2024)
- [Advances in Multimodal Adaptation and Generalization: From Traditional Approaches to Foundation Models](https://mlsanity.com/paper/2501.18592/) (2025)
- [Prompt-based Adaptation in Large-scale Vision Models: A Survey](https://mlsanity.com/paper/2510.13219/) (2025)
- [Holistic Evaluation of GPT-4V for Biomedical Imaging](https://mlsanity.com/paper/2312.05256/) (2023)
- [Medical Multimodal Foundation Models in Clinical Diagnosis and Treatment: Applications, Challenges, and Future Directions](https://mlsanity.com/paper/2412.02621/) (2024)
- [Parallels Between VLA Model Post-Training and Human Motor Learning: Progress, Challenges, and Trends](https://mlsanity.com/paper/2506.20966/) (2025)
- [Cross Prompting Consistency with Segment Anything Model for Semi-supervised Medical Image Segmentation](https://mlsanity.com/paper/2407.05416/) (2024)
- [Is SAM 2 Better than SAM in Medical Image Segmentation?](https://mlsanity.com/paper/2408.04212/) (2024)
- [A Comprehensive Survey of Mamba Architectures for Medical Image Analysis: Classification, Segmentation, Restoration and Beyond](https://mlsanity.com/paper/2410.02362/) (2024)
- [Dino U-Net: Exploiting High-Fidelity Dense Features from Foundation Models for Medical Image Segmentation](https://mlsanity.com/paper/2508.20909/) (2025)
- [ZePT: Zero-Shot Pan-Tumor Segmentation via Query-Disentangling and Self-Prompting](https://mlsanity.com/paper/2312.04964/) (2023)
- [On the Promises and Challenges of Multimodal Foundation Models for Geographical, Environmental, Agricultural, and Urban Planning Applications](https://mlsanity.com/paper/2312.17016/) (2023)
- [PRISM: A Promptable and Robust Interactive Segmentation Model with Visual Prompts](https://mlsanity.com/paper/2404.15028/) (2024)
- [EchoFM: Foundation Model for Generalizable Echocardiogram Analysis](https://mlsanity.com/paper/2410.23413/) (2024)
- [DC-SAM: In-Context Segment Anything in Images and Videos via Dual Consistency](https://mlsanity.com/paper/2504.12080/) (2025)
- [CAT: Coordinating Anatomical-Textual Prompts for Multi-Organ and Tumor Segmentation](https://mlsanity.com/paper/2406.07085/) (2024)
- [Biomedical SAM 2: Segment Anything in Biomedical Images and Videos](https://mlsanity.com/paper/2408.03286/) (2024)
- [SAM2 for Image and Video Segmentation: A Comprehensive Survey](https://mlsanity.com/paper/2503.12781/) (2025)
- [Towards a Comprehensive, Efficient and Promptable Anatomic Structure Segmentation Model using 3D Whole-body CT Scans](https://mlsanity.com/paper/2403.15063/) (2024)
- [Tri-Plane Mamba: Efficiently Adapting Segment Anything Model for 3D Medical Images](https://mlsanity.com/paper/2409.08492/) (2024)

## Abstract (arXiv)

The Segment Anything Model (SAM), a foundation model for general image segmentation, has demonstrated impressive zero-shot performance across numerous natural image segmentation tasks. However, SAM's performance significantly declines when applied to medical images, primarily due to the substantial disparity between natural and medical image domains. To effectively adapt SAM to medical images, it is important to incorporate critical third-dimensional information, i.e., volumetric or temporal knowledge, during fine-tuning. Simultaneously, we aim to harness SAM's pre-trained weights within its original 2D backbone to the fullest extent. In this paper, we introduce a modality-agnostic SAM adaptation framework, named as MA-SAM, that is applicable to various volumetric and video medical data. Our method roots in the parameter-efficient fine-tuning strategy to update only a small portion of weight increments while preserving the majority of SAM's pre-trained weights. By injecting a series of 3D adapters into the transformer blocks of the image encoder, our method enables the pre-trained 2D backbone to extract third-dimensional information from input data. The effectiveness of our method has been comprehensively evaluated on four medical image segmentation tasks, by using 10 public datasets across CT, MRI, and surgical video data. Remarkably, without using any prompt, our method consistently outperforms various state-of-the-art 3D approaches, surpassing nnU-Net by 0.9%, 2.6%, and 9.9% in Dice for CT multi-organ segmentation, MRI prostate segmentation, and surgical scene segmentation respectively. Our model also demonstrates strong generalization, and excels in challenging tumor segmentation when prompts are used. Our code is available at: https://github.com/cchen-cc/MA-SAM.