# MIQ-SAM3D: From Single-Point Prompt to Multi-Instance Segmentation via Competitive Query Refinement

arXiv: https://arxiv.org/abs/2511.01345 · HTML: https://mlsanity.com/paper/2511.01345/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 16 of its 22 references that are in the map.
- First posted on arXiv 3 Nov 2025.

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

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Masked-attention Mask Transformer for Universal Image Segmentation](https://mlsanity.com/paper/2112.01527/) (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)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [The Liver Tumor Segmentation Benchmark (LiTS)](https://mlsanity.com/paper/1901.04056/) (2019)
- [Segment Anything Model for Medical Image Analysis: an Experimental Study](https://mlsanity.com/paper/2304.10517/) (2023)
- [The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge](https://mlsanity.com/paper/1912.01054/) (2019)
- [UNETR++: Delving into Efficient and Accurate 3D Medical Image Segmentation](https://mlsanity.com/paper/2212.04497/) (2022)
- [3D UX-Net: A Large Kernel Volumetric ConvNet Modernizing Hierarchical Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2209.15076/) (2022)
- [Foundational Models in Medical Imaging: A Comprehensive Survey and Future Vision](https://mlsanity.com/paper/2310.18689/) (2023)
- [BEFUnet: A Hybrid CNN-Transformer Architecture for Precise Medical Image Segmentation](https://mlsanity.com/paper/2402.08793/) (2024)
- [Hierarchical Self-Prompting SAM: A Prompt-Free Medical Image Segmentation Framework](https://mlsanity.com/paper/2506.02854/) (2025)
- [SAM-aware Test-time Adaptation for Universal Medical Image Segmentation](https://mlsanity.com/paper/2506.05221/) (2025)

## Abstract (arXiv)

Accurate segmentation of medical images is fundamental to tumor diagnosis and treatment planning. SAM-based interactive segmentation has gained attention for its strong generalization, but most methods follow a single-point-to-single-object paradigm, which limits multi-lesion segmentation. Moreover, ViT backbones capture global context but often miss high-fidelity local details. We propose MIQ-SAM3D, a multi-instance 3D segmentation framework with a competitive query optimization strategy that shifts from single-point-to-single-mask to single-point-to-multi-instance. A prompt-conditioned instance-query generator transforms a single point prompt into multiple specialized queries, enabling retrieval of all semantically similar lesions across the 3D volume from a single exemplar. A hybrid CNN-Transformer encoder injects CNN-derived boundary saliency into ViT self-attention via spatial gating. A competitively optimized query decoder then enables end-to-end, parallel, multi-instance prediction through inter-query competition. On LiTS17 and KiTS21 dataset, MIQ-SAM3D achieved comparable levels and exhibits strong robustness to prompts, providing a practical solution for efficient annotation of clinically relevant multi-lesion cases.