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Paper · 2312.17183 · 2023

Large-Vocabulary Segmentation for Medical Images with Text Prompts

arXiv · PDF · Open in the Atlas

Code that ran

We lifted 3 functions out of this paper's own repositories and ran 2 of them in a sandbox. "Ran" means the function executed on a synthesized input and returned a value. It is not a reproduction of the paper's results.

RepositoryRoleRan
zhaoziheng/sat-ds canonical 2 of 3
FunctionStatusWhere it lives
Normalization Ran zhaoziheng/sat-ds/loader.py
pointer only (licence: NONE) · get_code("a6bc7496b6b250f9")
contains Ran zhaoziheng/sat-ds/train_test_split.py
pointer only (licence: NONE) · get_code("a518e29963d7ed31")
npy_loader Not yet run zhaoziheng/sat-ds/loader_npy.py
pointer only (licence: NONE) · get_code("321b45a28a2354f6")

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Abstract

This paper aims to build a model that can Segment Anything in 3D medical images, driven by medical terminologies as Text prompts, termed as SAT. Our main contributions are three-fold: (i) We construct the first multimodal knowledge tree on human anatomy, including 6502 anatomical terminologies; Then, we build the largest and most comprehensive segmentation dataset for training, collecting over 22K 3D scans from 72 datasets, across 497 classes, with careful standardization on both image and label space; (ii) We propose to inject medical knowledge into a text encoder via contrastive learning and formulate a large-vocabulary segmentation model that can be prompted by medical terminologies in text form; (iii) We train SAT-Nano (110M parameters) and SAT-Pro (447M parameters). SAT-Pro achieves comparable performance to 72 nnU-Nets -- the strongest specialist models trained on each dataset (over 2.2B parameters combined) -- over 497 categories. Compared with the interactive approach MedSAM, SAT-Pro consistently outperforms across all 7 human body regions with +7.1% average Dice Similarity Coefficient (DSC) improvement, while showing enhanced scalability and robustness. On 2 external (cross-center) datasets, SAT-Pro achieves higher performance than all baselines (+3.7% average DSC), demonstrating superior generalization ability.

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