# 3DSAM-adapter: Holistic adaptation of SAM from 2D to 3D for promptable tumor segmentation

arXiv: https://arxiv.org/abs/2306.13465 · HTML: https://mlsanity.com/paper/2306.13465/

## Key facts

- Cited by 70 papers in the map (data through 14 Oct 2026).
- Builds on 41 of its 58 references that are in the map.
- First posted on arXiv 23 Jun 2023.

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

- [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)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Hierarchical Text-Conditional Image Generation with CLIP Latents](https://mlsanity.com/paper/2204.06125/) (2022)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Parameter-Efficient Transfer Learning for NLP](https://mlsanity.com/paper/1902.00751/) (2019)
- [Pre-train, Prompt, and Predict: A Systematic Survey of Prompting Methods in Natural Language Processing](https://mlsanity.com/paper/2107.13586/) (2021)
- [Fourier Features Let Networks Learn High Frequency Functions in Low Dimensional Domains](https://mlsanity.com/paper/2006.10739/) (2020)
- [Visual Prompt Tuning](https://mlsanity.com/paper/2203.12119/) (2022)
- [Rethinking Semantic Segmentation from a Sequence-to-Sequence Perspective with Transformers](https://mlsanity.com/paper/2012.15840/) (2020)
- [BitFit: Simple Parameter-efficient Fine-tuning for Transformer-based Masked Language-models](https://mlsanity.com/paper/2106.10199/) (2021)
- [Self-supervised Visual Feature Learning with Deep Neural Networks: A Survey](https://mlsanity.com/paper/1902.06162/) (2019)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [Segment Everything Everywhere All at Once](https://mlsanity.com/paper/2304.06718/) (2023)
- [The Liver Tumor Segmentation Benchmark (LiTS)](https://mlsanity.com/paper/1901.04056/) (2019)
- [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)
- [Early Convolutions Help Transformers See Better](https://mlsanity.com/paper/2106.14881/) (2021)
- [Rethinking ImageNet Pre-training](https://mlsanity.com/paper/1811.08883/) (2018)
- [Parameter-Efficient Transfer Learning with Diff Pruning](https://mlsanity.com/paper/2012.07463/) (2020)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [Segment Anything Model for Medical Image Analysis: an Experimental Study](https://mlsanity.com/paper/2304.10517/) (2023)
- [TransBTS: Multimodal Brain Tumor Segmentation Using Transformer](https://mlsanity.com/paper/2103.04430/) (2021)
- [SegGPT: Segmenting Everything In Context](https://mlsanity.com/paper/2304.03284/) (2023)
- [ST-Adapter: Parameter-Efficient Image-to-Video Transfer Learning](https://mlsanity.com/paper/2206.13559/) (2022)
- [The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge](https://mlsanity.com/paper/1912.01054/) (2019)
- [AIM: Adapting Image Models for Efficient Video Action Recognition](https://mlsanity.com/paper/2302.03024/) (2023)

## Built on by (most cited first, 30 of 70)

- [Foundational Models Defining a New Era in Vision: A Survey and Outlook](https://mlsanity.com/paper/2307.13721/) (2023)
- [SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images](https://mlsanity.com/paper/2310.15161/) (2023)
- [Segment Anything Model for Medical Image Segmentation: Current Applications and Future Directions](https://mlsanity.com/paper/2401.03495/) (2024)
- [MedSAM2: Segment Anything in 3D Medical Images and Videos](https://mlsanity.com/paper/2504.03600/) (2025)
- [MA-SAM: Modality-agnostic SAM Adaptation for 3D Medical Image Segmentation](https://mlsanity.com/paper/2309.08842/) (2023)
- [Foundation Model for Advancing Healthcare: Challenges, Opportunities, and Future Directions](https://mlsanity.com/paper/2404.03264/) (2024)
- [Foundational Models in Medical Imaging: A Comprehensive Survey and Future Vision](https://mlsanity.com/paper/2310.18689/) (2023)
- [SA-Med2D-20M Dataset: Segment Anything in 2D Medical Imaging with 20 Million masks](https://mlsanity.com/paper/2311.11969/) (2023)
- [Unleashing the Potential of SAM for Medical Adaptation via Hierarchical Decoding](https://mlsanity.com/paper/2403.18271/) (2024)
- [Segment Anything in Medical Images and Videos: Benchmark and Deployment](https://mlsanity.com/paper/2408.03322/) (2024)
- [nnInteractive: Redefining 3D Promptable Segmentation](https://mlsanity.com/paper/2503.08373/) (2025)
- [Image Segmentation in Foundation Model Era: A Survey](https://mlsanity.com/paper/2408.12957/) (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)
- [Foundation Models for Biomedical Image Segmentation: A Survey](https://mlsanity.com/paper/2401.07654/) (2024)
- [Data-Centric Foundation Models in Computational Healthcare: A Survey](https://mlsanity.com/paper/2401.02458/) (2024)
- [Prompt-based Adaptation in Large-scale Vision Models: A Survey](https://mlsanity.com/paper/2510.13219/) (2025)
- [Self-Sampling Meta SAM: Enhancing Few-shot Medical Image Segmentation with Meta-Learning](https://mlsanity.com/paper/2308.16466/) (2023)
- [Promise:Prompt-driven 3D Medical Image Segmentation Using Pretrained Image Foundation Models](https://mlsanity.com/paper/2310.19721/) (2023)
- [Medical Multimodal Foundation Models in Clinical Diagnosis and Treatment: Applications, Challenges, and Future Directions](https://mlsanity.com/paper/2412.02621/) (2024)
- [MedSAM-U: Uncertainty-Guided Auto Multi-Prompt Adaptation for Reliable MedSAM](https://mlsanity.com/paper/2409.00924/) (2024)
- [EndoSparse: Real-Time Sparse View Synthesis of Endoscopic Scenes using Gaussian Splatting](https://mlsanity.com/paper/2407.01029/) (2024)
- [PRISM: A Promptable and Robust Interactive Segmentation Model with Visual Prompts](https://mlsanity.com/paper/2404.15028/) (2024)
- [MAS-SAM: Segment Any Marine Animal with Aggregated Features](https://mlsanity.com/paper/2404.15700/) (2024)
- [ROS-SAM: High-Quality Interactive Segmentation for Remote Sensing Moving Object](https://mlsanity.com/paper/2503.12006/) (2025)
- [Kernel-based Unsupervised Embedding Alignment for Enhanced Visual Representation in Vision-language Models](https://mlsanity.com/paper/2506.02557/) (2025)
- [A Foundation Model for Brain Lesion Segmentation with Mixture of Modality Experts](https://mlsanity.com/paper/2405.10246/) (2024)
- [Segment Anything with Multiple Modalities](https://mlsanity.com/paper/2408.09085/) (2024)
- [LesionLocator: Zero-Shot Universal Tumor Segmentation and Tracking in 3D Whole-Body Imaging](https://mlsanity.com/paper/2502.20985/) (2025)
- [GoodSAM++: Bridging Domain and Capacity Gaps via Segment Anything Model for Panoramic Semantic Segmentation](https://mlsanity.com/paper/2408.09115/) (2024)
- [SegAnyPET: Universal Promptable Segmentation from Positron Emission Tomography Images](https://mlsanity.com/paper/2502.14351/) (2025)

## Abstract (arXiv)

Despite that the segment anything model (SAM) achieved impressive results on general-purpose semantic segmentation with strong generalization ability on daily images, its demonstrated performance on medical image segmentation is less precise and not stable, especially when dealing with tumor segmentation tasks that involve objects of small sizes, irregular shapes, and low contrast. Notably, the original SAM architecture is designed for 2D natural images, therefore would not be able to extract the 3D spatial information from volumetric medical data effectively. In this paper, we propose a novel adaptation method for transferring SAM from 2D to 3D for promptable medical image segmentation. Through a holistically designed scheme for architecture modification, we transfer the SAM to support volumetric inputs while retaining the majority of its pre-trained parameters for reuse. The fine-tuning process is conducted in a parameter-efficient manner, wherein most of the pre-trained parameters remain frozen, and only a few lightweight spatial adapters are introduced and tuned. Regardless of the domain gap between natural and medical data and the disparity in the spatial arrangement between 2D and 3D, the transformer trained on natural images can effectively capture the spatial patterns present in volumetric medical images with only lightweight adaptations. We conduct experiments on four open-source tumor segmentation datasets, and with a single click prompt, our model can outperform domain state-of-the-art medical image segmentation models on 3 out of 4 tasks, specifically by 8.25%, 29.87%, and 10.11% for kidney tumor, pancreas tumor, colon cancer segmentation, and achieve similar performance for liver tumor segmentation. We also compare our adaptation method with existing popular adapters, and observed significant performance improvement on most datasets.