nnInteractive Agent: General-Purpose AI Agents as 3D Image Annotators

cs.LG Fabian Isensee, Constantin Ulrich Harsy, Maximilian Rokuss, Benjamin Hamm, Philipp Vollmuth, Klaus H. Maier-Hein · Oct 22, 2026

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Code: https://github. com/MIC-DKFZ/nninteractive-agent

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Abstract

Interactive 3D segmentation models such as nnInteractive turn a few spatial prompts (points, scribbles, boxes) into accurate volumetric masks, but a human still does the annotation work: finding each structure, placing prompts, checking the result and correcting it. General-purpose AI agents can now interpret images, call tools and write code. We show that such agents can take over this work without additional training: the user makes a request in plain language, and the agent works out what has to be segmented, locates the targets, prompts nnInteractive, inspects the 3D result, corrects it and responds to feedback. Asked for 'the muscles used for chewing', an agent identifies and segments the masseters and pterygoids; asked to count liver lesions, it writes its own code to find candidates and splits a merged lesion on request. Our open-source nninteractive-agent provides nnInteractive as tools over the Model Context Protocol (MCP), together with a skill that encodes how experienced users prompt it. On a benchmark spanning CT, MRI, PET and micro-CT of humans, a mouse and an ant (14 images; 51 targets from organs and tumours to muscles, foot bones, vessel trees and an insect brain), Claude Code and Codex reach a mean Dice of 0.81 and 0.84 from the request alone; when told where each target is, both reach 0.85 and prompt nearly as effectively as an oracle that places prompts using the reference segmentation. A text-prompted 3D model (VoxTell) is more accurate on most standard radiological targets but less robust: it returns an empty mask for one of them and fails on the leg muscles, the foot bones, the mouse and the ant, where the agents remain accurate. Code: https://github.com/MIC-DKFZ/nninteractive-agent

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