# MultiverSeg: Scalable Interactive Segmentation of Biomedical Imaging Datasets with In-Context Guidance

arXiv: https://arxiv.org/abs/2412.15058 · HTML: https://mlsanity.com/paper/2412.15058/

## Key facts

- Cited by 13 papers in the map (data through 14 Oct 2026).
- Builds on 70 of its 143 references that are in the map.
- First posted on arXiv 19 Dec 2024.

## Builds on (most cited first, 30 of 70)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [SAM 2: Segment Anything in Images and Videos](https://mlsanity.com/paper/2408.00714/) (2024)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [Skin Lesion Analysis Toward Melanoma Detection: A Challenge at the 2017 International Symposium on Biomedical Imaging (ISBI), Hosted by the International Skin Imaging Collaboration (ISIC)](https://mlsanity.com/paper/1710.05006/) (2017)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [The Liver Tumor Segmentation Benchmark (LiTS)](https://mlsanity.com/paper/1901.04056/) (2019)
- [Medical SAM Adapter: Adapting Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.12620/) (2023)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [A large annotated medical image dataset for the development and evaluation of segmentation algorithms](https://mlsanity.com/paper/1902.09063/) (2019)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [ScribbleSup: Scribble-Supervised Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1604.05144/) (2016)
- [CHAOS Challenge -- Combined (CT-MR) Healthy Abdominal Organ Segmentation](https://mlsanity.com/paper/2001.06535/) (2020)
- [Customized Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.13785/) (2023)
- [Deep Learning for Segmentation using an Open Large-Scale Dataset in 2D Echocardiography](https://mlsanity.com/paper/1908.06948/) (2019)
- [SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining](https://mlsanity.com/paper/2107.09559/) (2021)
- [Validation, comparison, and combination of algorithms for automatic detection of pulmonary nodules in computed tomography images: the LUNA16 challenge](https://mlsanity.com/paper/1612.08012/) (2016)
- [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)
- [Reviving Iterative Training with Mask Guidance for Interactive Segmentation](https://mlsanity.com/paper/2102.06583/) (2021)
- [Deep Interactive Object Selection](https://mlsanity.com/paper/1603.04042/) (2016)
- [BoxInst: High-Performance Instance Segmentation with Box Annotations](https://mlsanity.com/paper/2012.02310/) (2020)
- [Data augmentation using learned transformations for one-shot medical image segmentation](https://mlsanity.com/paper/1902.09383/) (2019)
- [f-BRS: Rethinking Backpropagating Refinement for Interactive Segmentation](https://mlsanity.com/paper/2001.10331/) (2020)
- [Standardized Assessment of Automatic Segmentation of White Matter Hyperintensities and Results of the WMH Segmentation Challenge](https://mlsanity.com/paper/1904.00682/) (2019)
- [PanNuke Dataset Extension, Insights and Baselines](https://mlsanity.com/paper/2003.10778/) (2020)
- [Interactive Medical Image Segmentation using Deep Learning with Image-specific Fine-tuning](https://mlsanity.com/paper/1710.04043/) (2017)
- [SimpleClick: Interactive Image Segmentation with Simple Vision Transformers](https://mlsanity.com/paper/2210.11006/) (2022)
- [DeepIGeoS: A Deep Interactive Geodesic Framework for Medical Image Segmentation](https://mlsanity.com/paper/1707.00652/) (2017)
- [Large-scale interactive object segmentation with human annotators](https://mlsanity.com/paper/1903.10830/) (2019)

## Built on by (most cited first, 13 of 13)

- [MedCLIPSeg: Probabilistic Vision-Language Adaptation for Data-Efficient and Generalizable Medical Image Segmentation](https://mlsanity.com/paper/2602.20423/) (2026)
- [K-Prism: A Knowledge-Guided and Prompt Integrated Universal Medical Image Segmentation Model](https://mlsanity.com/paper/2509.25594/) (2025)
- [Atlas is Your Perfect Context: One-Shot Customization for Generalizable Foundational Medical Image Segmentation](https://mlsanity.com/paper/2512.18176/) (2025)
- [Mask to Concept: Auto-Promptable SAM3 via Efficient Test-Time Concept Embedding Search for Few-Shot Annotation](https://mlsanity.com/paper/2606.26711/) (2026)
- [Expert-like Bone Ultrasound Segmentation through Expert-in-the-loop Mask-conditioned Progressive Learning](https://mlsanity.com/paper/2609.00473/) (2026)
- [Pancakes: Consistent Multi-Protocol Image Segmentation Across Biomedical Domains](https://mlsanity.com/paper/2512.13534/) (2025)
- [CLoPA: Continual Low Parameter Adaptation of Interactive Segmentation for Medical Image Annotation](https://mlsanity.com/paper/2603.06426/) (2026)
- [Why Invariance is Not Enough for Biomedical Domain Generalization and How to Fix It](https://mlsanity.com/paper/2604.02564/) (2026)
- [SD-FSMIS: Adapting Stable Diffusion for Few-Shot Medical Image Segmentation](https://mlsanity.com/paper/2604.03134/) (2026)
- [UniMedSeg: Unified In-Context Learning for Multi-Paradigm 2D/3D Medical Image Segmentation](https://mlsanity.com/paper/2607.12896/) (2026)
- [From Few-Shot Segmentation to Clinician-in-the-Loop Medical Image Analysis](https://mlsanity.com/paper/2609.10001/) (2026)
- [UniPro: Unified Multi-Mode Medical Image Segmentation from 2D Images to 3D Volumes via Propagation](https://mlsanity.com/paper/2610.06938/) (2026)
- [From Human Corrections to Learned Segmentations: A Critical Mathematical Review of Information, Learning, and Human Effort](https://mlsanity.com/paper/2610.20396/) (2026)

## Abstract (arXiv)

Medical researchers and clinicians often need to perform novel segmentation tasks on a set of related images. Existing methods for segmenting a new dataset are either interactive, requiring substantial human effort for each image, or require an existing set of previously labeled images. We introduce a system, MultiverSeg, that enables practitioners to rapidly segment an entire new dataset without requiring access to any existing labeled data from that task or domain. Along with the image to segment, the model takes user interactions such as clicks, bounding boxes or scribbles as input, and predicts a segmentation. As the user segments more images, those images and segmentations become additional inputs to the model, providing context. As the context set of labeled images grows, the number of interactions required to segment each new image decreases. We demonstrate that MultiverSeg enables users to interactively segment new datasets efficiently, by amortizing the number of interactions per image to achieve an accurate segmentation. Compared to using a state-of-the-art interactive segmentation method, MultiverSeg reduced the total number of clicks by 36% and scribble steps by 25% to achieve 90% Dice on sets of images from unseen tasks. We release code and model weights at https://multiverseg.csail.mit.edu