Abstract
Segmentation of 3D medical images is a labor-intensive task with important clinical applications. Recently, foundation models for image segmentation have received significant interest. Specifically, many works have proposed methods for the adaptation of promptable natural image foundation models to medical image segmentation. However, the shift to 3D volumes from 2D natural images has proven difficult, and many approaches have limited real-world clinical applicability due to large model sizes and corresponding heavy computational requirements. Here, we present an original model for generalized, promptable 3D medical image segmentation. Our approach leverages a lightweight convolutional backbone while simultaneously integrating information from single-point prompts at multiple spatial resolutions. Our approach dramatically reduces the computational burden for promptable segmentation while also outperforming similar recent works on a diverse dataset of 98,699 image-mask pairs from CT and MRI datasets.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Baid, U., Ghodasara, S., Mohan, S., Bilello, M., Calabrese, E., Colak, E., Farahani, K., Kalpathy-Cramer, J., Kitamura, F.C., Pati, S., et al.: The rsna-asnr-miccai brats 2021 benchmark on brain tumor segmentation and radiogenomic classification. arXiv preprint arXiv:2107.02314 (2021)
Bakas, S., Akbari, H., Sotiras, A., Bilello, M., Rozycki, M., Kirby, J.S., Freymann, J.B., Farahani, K., Davatzikos, C.: Advancing the cancer genome atlas glioma mri collections with expert segmentation labels and radiomic features. Scientific data 4(1), 1–13 (2017)
Cardenas, C.E., Yang, J., Anderson, B.M., Court, L.E., Brock, K.B.: Advances in auto-segmentation. In: Seminars in radiation oncology. vol. 29, pp. 185–197. Elsevier (2019)
Cheng, J., Ye, J., Deng, Z., Chen, J., Li, T., Wang, H., Su, Y., Huang, Z., Chen, J., Jiang, L., et al.: Sam-med2d. arXiv preprint arXiv:2308.16184 (2023)
Dosovitskiy, A., Beyer, L., Kolesnikov, A., Weissenborn, D., Zhai, X., Unterthiner, T., Dehghani, M., Minderer, M., Heigold, G., Gelly, S., et al.: An image is worth 16x16 words: Transformers for image recognition at scale. arXiv preprint arXiv:2010.11929 (2020)
Finn, C., Abbeel, P., Levine, S.: Model-agnostic meta-learning for fast adaptation of deep networks. In: International conference on machine learning. pp. 1126–1135. PMLR (2017)
He, K., Chen, X., Xie, S., Li, Y., Dollár, P., Girshick, R.: Masked autoencoders are scalable vision learners. In: Proceedings of the IEEE/CVF conference on computer vision and pattern recognition. pp. 16000–16009 (2022)
Ji, Y., Bai, H., Ge, C., Yang, J., Zhu, Y., Zhang, R., Li, Z., Zhanng, L., Ma, W., Wan, X., et al.: Amos: A large-scale abdominal multi-organ benchmark for versatile medical image segmentation. Adv. Neural. Inf. Process. Syst. 35, 36722–36732 (2022)
Kirillov, A., Mintun, E., Ravi, N., Mao, H., Rolland, C., Gustafson, L., Xiao, T., Whitehead, S., Berg, A.C., Lo, W.Y., et al.: Segment anything. In: Proceedings of the IEEE/CVF International Conference on Computer Vision. pp. 4015–4026 (2023)
Ma, J., He, Y., Li, F., Han, L., You, C., Wang, B.: Segment anything in medical images. Nat. Commun. 15(1), 654 (2024)
Mazurowski, M.A., Dong, H., Gu, H., Yang, J., Konz, N., Zhang, Y.: Segment anything model for medical image analysis: an experimental study. Med. Image Anal. 89, 102918 (2023)
Menze, B.H., Jakab, A., Bauer, S., Kalpathy-Cramer, J., Farahani, K., Kirby, J., Burren, Y., Porz, N., Slotboom, J., Wiest, R., et al.: The multimodal brain tumor image segmentation benchmark (brats). IEEE Trans. Med. Imaging 34(10), 1993–2024 (2014)
Shen, Y., Li, J., Shao, X., Romillo, B.I., Jindal, A., Dreizin, D., Unberath, M.: Fastsam3d: An efficient segment anything model for 3d volumetric medical images. arXiv preprint arXiv:2403.09827 (2024)
Wang, H., Guo, S., Ye, J., Deng, Z., Cheng, J., Li, T., Chen, J., Su, Y., Huang, Z., Shen, Y., Fu, B., Zhang, S., He, J., Qiao, Y.: Sam-med3d. arXiv preprint arXiv:2310.15161v2 (2024)
Wasserthal, J., Breit, H.C., Meyer, M.T., Pradella, M., Hinck, D., Sauter, A.W., Heye, T., Boll, D.T., Cyriac, J., Yang, S., et al.: Totalsegmentator: robust segmentation of 104 anatomic structures in ct images. Radiology: Artificial Intelligence 5(5) (2023)
Zhou, L., Liu, H., Bae, J., He, J., Samaras, D., Prasanna, P.: Self pre-training with masked autoencoders for medical image classification and segmentation. In: 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI). pp. 1–6. IEEE (2023)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2025 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this paper
Cite this paper
Bae, J., Guo, X., Yerebakan, H., Shinagawa, Y., Farhand, S. (2025). SAMU: An Efficient and Promptable Foundation Model for Medical Image Segmentation. In: Deng, Z., et al. Foundation Models for General Medical AI. MedAGI 2024. Lecture Notes in Computer Science, vol 15184. Springer, Cham. https://doi.org/10.1007/978-3-031-73471-7_14
Download citation
DOI: https://doi.org/10.1007/978-3-031-73471-7_14
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-031-73470-0
Online ISBN: 978-3-031-73471-7
eBook Packages: Computer ScienceComputer Science (R0)