# ShapeMamba-EM: Fine-Tuning Foundation Model with Local Shape Descriptors and Mamba Blocks for 3D EM Image Segmentation

arXiv: https://arxiv.org/abs/2408.14114 · HTML: https://mlsanity.com/paper/2408.14114/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Placed in Mamba for medical image analysis, one of 10 directions in State-space sequence models (S4, Mamba).
- Builds on 16 of its 30 references that are in the map.
- First posted on arXiv 26 Aug 2024.

## Placed in

- State-space sequence models (S4, Mamba) / [Mamba for medical image analysis](https://mlsanity.com/ssm/mamba-for-medical-image-analysis/)

## Builds on (most cited first, 16 of 16)

- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://mlsanity.com/paper/2312.00752/) (2023)
- [Efficiently Modeling Long Sequences with Structured State Spaces](https://mlsanity.com/paper/2111.00396/) (2021)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [Medical SAM Adapter: Adapting Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.12620/) (2023)
- [U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation](https://mlsanity.com/paper/2401.04722/) (2024)
- [FacT: Factor-Tuning for Lightweight Adaptation on Vision Transformer](https://mlsanity.com/paper/2212.03145/) (2022)
- [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)
- [MA-SAM: Modality-agnostic SAM Adaptation for 3D Medical Image Segmentation](https://mlsanity.com/paper/2309.08842/) (2023)
- [3DSAM-adapter: Holistic adaptation of SAM from 2D to 3D for promptable tumor segmentation](https://mlsanity.com/paper/2306.13465/) (2023)
- [Superhuman Accuracy on the SNEMI3D Connectomics Challenge](https://mlsanity.com/paper/1706.00120/) (2017)
- [Visual Query Tuning: Towards Effective Usage of Intermediate Representations for Parameter and Memory Efficient Transfer Learning](https://mlsanity.com/paper/2212.03220/) (2022)
- [VLN-PETL: Parameter-Efficient Transfer Learning for Vision-and-Language Navigation](https://mlsanity.com/paper/2308.10172/) (2023)
- [NucMM Dataset: 3D Neuronal Nuclei Instance Segmentation at Sub-Cubic Millimeter Scale](https://mlsanity.com/paper/2107.05840/) (2021)

## Built on by (most cited first, 3 of 3)

- [DefMamba: Deformable Visual State Space Model](https://mlsanity.com/paper/2504.05794/) (2025)
- [MSD-KMamba: Bidirectional Spatial-Aware Multi-Modal 3D Brain Segmentation via Multi-scale Self-Distilled Fusion Strategy](https://mlsanity.com/paper/2509.23677/) (2025)
- [TEAMS: Text-prompted spatiotEmporal dual-heAd Mamba Snake](https://mlsanity.com/paper/2608.17421/) (2026)

## Abstract (arXiv)

Electron microscopy (EM) imaging offers unparalleled resolution for analyzing neural tissues, crucial for uncovering the intricacies of synaptic connections and neural processes fundamental to understanding behavioral mechanisms. Recently, the foundation models have demonstrated impressive performance across numerous natural and medical image segmentation tasks. However, applying these foundation models to EM segmentation faces significant challenges due to domain disparities. This paper presents ShapeMamba-EM, a specialized fine-tuning method for 3D EM segmentation, which employs adapters for long-range dependency modeling and an encoder for local shape description within the original foundation model. This approach effectively addresses the unique volumetric and morphological complexities of EM data. Tested over a wide range of EM images, covering five segmentation tasks and 10 datasets, ShapeMamba-EM outperforms existing methods, establishing a new standard in EM image segmentation and enhancing the understanding of neural tissue architecture.