SAM4EM: Efficient memory-based two stage prompt-free segment anything model adapter for complex 3D neuroscience electron microscopy stacks

Uzair Shah; Marco Agus; Daniya Boges; Vanessa Chiappini; Mahmood Alzubaidi; Jens Schneider; Markus Hadwiger; Pierre J. Magistretti; Mowafa Househ; Corrado Calı

arXiv · 2504.21544

SAM4EM: Efficient memory-based two stage prompt-free segment anything model adapter for complex 3D neuroscience electron microscopy stacks

Uzair Shah·Marco Agus·Daniya Boges·Vanessa Chiappini·Mahmood Alzubaidi·Jens Schneider·Markus Hadwiger·Pierre J. Magistretti·Mowafa Househ·Corrado Calı

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Abstract

We present SAM4EM, a novel approach for 3D segmentation of complex neural structures in electron microscopy (EM) data by leveraging the Segment Anything Model (SAM) alongside advanced fine-tuning strategies. Our contributions include the development of a prompt-free adapter for SAM using two stage mask decoding to automatically generate prompt embeddings, a dual-stage fine-tuning method based on Low-Rank Adaptation (LoRA) for enhancing segmentation with limited annotated data, and a 3D memory attention mechanism to ensure segmentation consistency across 3D stacks. We further release a unique benchmark dataset for the segmentation of astrocytic processes and synapses. We evaluated our method on challenging neuroscience segmentation benchmarks, specifically targeting mitochondria, glia, and synapses, with significant accuracy improvements over state-of-the-art (SOTA) methods, including recent SAM-based adapters developed for the medical domain and other vision transformer-based approaches. Experimental results indicate that our approach outperforms existing solutions in the segmentation of complex processes like glia and post-synaptic densities. Our code and models are available at https://github.com/Uzshah/SAM4EM.

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Uzair Shah, Marco Agus, Daniya Boges, Vanessa Chiappini, Mahmood Alzubaidi, Jens Schneider, Markus Hadwiger, Pierre J. Magistretti, Mowafa Househ, Corrado Calı. 2025-04-30. SAM4EM: Efficient memory-based two stage prompt-free segment anything model adapter for complex 3D neuroscience electron microscopy stacks. https://arxiv.org/abs/2504.21544

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