# Training-free CryoET Tomogram Segmentation

arXiv: https://arxiv.org/abs/2407.06833 · HTML: https://mlsanity.com/paper/2407.06833/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 9 of its 30 references that are in the map.
- First posted on arXiv 8 Jul 2024.

## Builds on (most cited first, 9 of 9)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Segment Everything Everywhere All at Once](https://mlsanity.com/paper/2304.06718/) (2023)
- [LERF: Language Embedded Radiance Fields](https://mlsanity.com/paper/2303.09553/) (2023)
- [Towards Robust Referring Video Object Segmentation with Cyclic Relational Consensus](https://mlsanity.com/paper/2207.01203/) (2022)
- [QDFormer: Towards Robust Audiovisual Segmentation in Complex Environments with Quantization-based Semantic Decomposition](https://mlsanity.com/paper/2310.00132/) (2023)
- [Hybrid Instance-aware Temporal Fusion for Online Video Instance Segmentation](https://mlsanity.com/paper/2112.01695/) (2021)

## Abstract (arXiv)

Cryogenic Electron Tomography (CryoET) is a useful imaging technology in structural biology that is hindered by its need for manual annotations, especially in particle picking. Recent works have endeavored to remedy this issue with few-shot learning or contrastive learning techniques. However, supervised training is still inevitable for them. We instead choose to leverage the power of existing 2D foundation models and present a novel, training-free framework, CryoSAM. In addition to prompt-based single-particle instance segmentation, our approach can automatically search for similar features, facilitating full tomogram semantic segmentation with only one prompt. CryoSAM is composed of two major parts: 1) a prompt-based 3D segmentation system that uses prompts to complete single-particle instance segmentation recursively with Cross-Plane Self-Prompting, and 2) a Hierarchical Feature Matching mechanism that efficiently matches relevant features with extracted tomogram features. They collaborate to enable the segmentation of all particles of one category with just one particle-specific prompt. Our experiments show that CryoSAM outperforms existing works by a significant margin and requires even fewer annotations in particle picking. Further visualizations demonstrate its ability when dealing with full tomogram segmentation for various subcellular structures. Our code is available at: https://github.com/xulabs/aitom