# nnInteractive: Redefining 3D Promptable Segmentation

arXiv: https://arxiv.org/abs/2503.08373 · HTML: https://mlsanity.com/paper/2503.08373/

## Key facts

- Cited by 41 papers in the map (data through 14 Oct 2026).
- Builds on 50 of its 132 references that are in the map.
- First posted on arXiv 11 Mar 2025.

## Builds on (most cited first, 30 of 50)

- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [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)
- [Deep Learning for Segmentation using an Open Large-Scale Dataset in 2D Echocardiography](https://mlsanity.com/paper/1908.06948/) (2019)
- [nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation](https://mlsanity.com/paper/2404.09556/) (2024)
- [AbdomenCT-1K: Is Abdominal Organ Segmentation A Solved Problem?](https://mlsanity.com/paper/2010.14808/) (2020)
- [DeepOrgan: Multi-level Deep Convolutional Networks for Automated Pancreas Segmentation](https://mlsanity.com/paper/1506.06448/) (2015)
- [Standardized Assessment of Automatic Segmentation of White Matter Hyperintensities and Results of the WMH Segmentation Challenge](https://mlsanity.com/paper/1904.00682/) (2019)
- [VerSe: A Vertebrae Labelling and Segmentation Benchmark for Multi-detector CT Images](https://mlsanity.com/paper/2001.09193/) (2020)
- [The KiTS21 Challenge: Automatic segmentation of kidneys, renal tumors, and renal cysts in corticomedullary-phase CT](https://mlsanity.com/paper/2307.01984/) (2023)
- [STU-Net: Scalable and Transferable Medical Image Segmentation Models Empowered by Large-Scale Supervised Pre-training](https://mlsanity.com/paper/2304.06716/) (2023)
- [MedPerf: Open Benchmarking Platform for Medical Artificial Intelligence using Federated Evaluation](https://mlsanity.com/paper/2110.01406/) (2021)
- [SegVol: Universal and Interactive Volumetric Medical Image Segmentation](https://mlsanity.com/paper/2311.13385/) (2023)
- [Association of genomic subtypes of lower-grade gliomas with shape features automatically extracted by a deep learning algorithm](https://mlsanity.com/paper/1906.03720/) (2019)
- [3DSAM-adapter: Holistic adaptation of SAM from 2D to 3D for promptable tumor segmentation](https://mlsanity.com/paper/2306.13465/) (2023)
- [CycleMix: A Holistic Strategy for Medical Image Segmentation from Scribble Supervision](https://mlsanity.com/paper/2203.01475/) (2022)
- [An automatic multi-tissue human fetal brain segmentation benchmark using the Fetal Tissue Annotation Dataset](https://mlsanity.com/paper/2010.15526/) (2020)
- [A New 2.5D Representation for Lymph Node Detection using Random Sets of Deep Convolutional Neural Network Observations](https://mlsanity.com/paper/1406.2639/) (2014)
- [AbdomenAtlas-8K: Annotating 8,000 CT Volumes for Multi-Organ Segmentation in Three Weeks](https://mlsanity.com/paper/2305.09666/) (2023)
- [Unleashing the Strengths of Unlabeled Data in Pan-cancer Abdominal Organ Quantification: the FLARE22 Challenge](https://mlsanity.com/paper/2308.05862/) (2023)
- [The TopCoW Challenge -- Topology-Aware Circle of Willis Segmentation for CT and MR Angiography](https://mlsanity.com/paper/2312.17670/) (2023)
- [ScribblePrompt: Fast and Flexible Interactive Segmentation for Any Biomedical Image](https://mlsanity.com/paper/2312.07381/) (2023)
- [MultiTalent: A Multi-Dataset Approach to Medical Image Segmentation](https://mlsanity.com/paper/2303.14444/) (2023)
- [SKM-TEA: A Dataset for Accelerated MRI Reconstruction with Dense Image Labels for Quantitative Clinical Evaluation](https://mlsanity.com/paper/2203.06823/) (2022)
- [Cardiac Segmentation on Late Gadolinium Enhancement MRI: A Benchmark Study from Multi-Sequence Cardiac MR Segmentation Challenge](https://mlsanity.com/paper/2006.12434/) (2020)
- [A large-scale multicenter breast cancer DCE-MRI benchmark dataset with expert segmentations](https://mlsanity.com/paper/2406.13844/) (2024)
- [Touchstone Benchmark: Are We on the Right Way for Evaluating AI Algorithms for Medical Segmentation?](https://mlsanity.com/paper/2411.03670/) (2024)

## Built on by (most cited first, 30 of 41)

- [MedSAM2: Segment Anything in 3D Medical Images and Videos](https://mlsanity.com/paper/2504.03600/) (2025)
- [Render-FM: Feedforward Model for Real-time Photorealistic Volumetric Rendering](https://mlsanity.com/paper/2505.17338/) (2025)
- [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)
- [PolyPose: Deformable 2D/3D Registration via Polyrigid Transformations](https://mlsanity.com/paper/2505.19256/) (2025)
- [Rethinking Whole-Body CT Image Interpretation: An Abnormality-Centric Approach](https://mlsanity.com/paper/2506.03238/) (2025)
- [ENSAM: an efficient foundation model for interactive segmentation of 3D medical images](https://mlsanity.com/paper/2509.15874/) (2025)
- [Dynamic Prompt Generation for Interactive 3D Medical Image Segmentation Training](https://mlsanity.com/paper/2510.03189/) (2025)
- [MeisenMeister: A Simple Two Stage Pipeline for Breast Cancer Classification on MRI](https://mlsanity.com/paper/2510.27326/) (2025)
- [BackSplit: The Importance of Sub-dividing the Background in Biomedical Lesion Segmentation](https://mlsanity.com/paper/2511.19394/) (2025)
- [On The Robustness of Foundational 3D Medical Image Segmentation Models Against Imprecise Visual Prompts](https://mlsanity.com/paper/2601.16383/) (2026)
- [TopoSculpt: Betti-Steered Topological Sculpting of 3D Fine-grained Tubular Shapes](https://mlsanity.com/paper/2509.03938/) (2025)
- [Efficient Universal Models for Medical Image Segmentation via Weakly Supervised In-Context Learning](https://mlsanity.com/paper/2510.05899/) (2025)
- [Medal S: Spatio-Textual Prompt Model for Medical Segmentation](https://mlsanity.com/paper/2511.13001/) (2025)
- [Finally Outshining the Random Baseline: A Simple and Effective Solution for Active Learning in 3D Biomedical Imaging](https://mlsanity.com/paper/2601.13677/) (2026)
- [Universality Reconsidered: Rethinking the Validation of Foundation Models for General-Purpose 3D Medical Segmentation](https://mlsanity.com/paper/2602.07643/) (2026)
- [3DLAND: 3D Lesion Abdominal Anomaly Localization Dataset](https://mlsanity.com/paper/2602.12820/) (2026)
- [Developing Foundation Models for Universal Segmentation from 3D Whole-Body Positron Emission Tomography](https://mlsanity.com/paper/2603.11627/) (2026)
- [RAPS-3D: Efficient interactive segmentation for 3D radiological imaging](https://mlsanity.com/paper/2507.07730/) (2025)
- [Promptable Longitudinal Lesion Segmentation in Whole-Body CT](https://mlsanity.com/paper/2509.00613/) (2025)
- [Visionerves: Automatic and Reproducible Hybrid AI for Peripheral Nervous System Recognition Applied to Endometriosis Cases](https://mlsanity.com/paper/2509.18185/) (2025)
- [MOIS-SAM2: Exemplar-based Segment Anything Model 2 for multilesion interactive segmentation of neurofibromas in whole-body MRI](https://mlsanity.com/paper/2509.19277/) (2025)
- [Domain-Specialized Interactive Segmentation Framework for Meningioma Radiotherapy Planning](https://mlsanity.com/paper/2510.00416/) (2025)
- [Resource-efficient Automatic Refinement of Segmentations via Weak Supervision from Light Feedback](https://mlsanity.com/paper/2511.02576/) (2025)
- [CLoPA: Continual Low Parameter Adaptation of Interactive Segmentation for Medical Image Annotation](https://mlsanity.com/paper/2603.06426/) (2026)
- [Foundation Model-guided Iteratively Prompting and Pseudo-Labeling for Partially Labeled Medical Image Segmentation](https://mlsanity.com/paper/2604.01038/) (2026)
- [Why Invariance is Not Enough for Biomedical Domain Generalization and How to Fix It](https://mlsanity.com/paper/2604.02564/) (2026)
- [CrossPan: A Comprehensive Benchmark for Cross-Sequence Pancreas MRI Segmentation and Generalization](https://mlsanity.com/paper/2604.18797/) (2026)
- [RoadGIE: Towards A Global-Scale Aerial Benchmark for Generalizable Interactive Road Extraction](https://mlsanity.com/paper/2605.26862/) (2026)
- [POPSICLE: Benchmark Datasets for Segmentation and Localization in CryoET](https://mlsanity.com/paper/2606.10255/) (2026)

## Abstract (arXiv)

Accurate and efficient 3D segmentation is essential for both clinical and research applications. While foundation models like SAM have revolutionized interactive segmentation, their 2D design and domain shift limitations make them ill-suited for 3D medical images. Current adaptations address some of these challenges but remain limited, either lacking volumetric awareness, offering restricted interactivity, or supporting only a small set of structures and modalities. Usability also remains a challenge, as current tools are rarely integrated into established imaging platforms and often rely on cumbersome web-based interfaces with restricted functionality. We introduce nnInteractive, the first comprehensive 3D interactive open-set segmentation method. It supports diverse prompts-including points, scribbles, boxes, and a novel lasso prompt-while leveraging intuitive 2D interactions to generate full 3D segmentations. Trained on 120+ diverse volumetric 3D datasets (CT, MRI, PET, 3D Microscopy, etc.), nnInteractive sets a new state-of-the-art in accuracy, adaptability, and usability. Crucially, it is the first method integrated into widely used image viewers (e.g., Napari, MITK), ensuring broad accessibility for real-world clinical and research applications. Extensive benchmarking demonstrates that nnInteractive far surpasses existing methods, setting a new standard for AI-driven interactive 3D segmentation. nnInteractive is publicly available: https://github.com/MIC-DKFZ/napari-nninteractive (Napari plugin), https://www.mitk.org/MITK-nnInteractive (MITK integration), https://github.com/MIC-DKFZ/nnInteractive (Python backend).