How do I install the Nnunet skill?

Run npx skillmds@latest add mkurman/nnunet in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

What does the Nnunet skill do?

No New U-Net — self-configuring framework for medical image segmentation. Automatically adapts to any dataset. Top performer on biomedical segmentation benchmarks (BraTS, KiTS, etc.). It is listed under AI & ML on SkillMD.

Is Nnunet safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Nnunet?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Nnunet free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Nnunet?

mkurman (@mkurman) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Nnunet by mkurman — Agent Skill

Name: Nnunet
Author: mkurman

File contents

Overview

nnUNet (No New U-Net) is a self-configuring framework for medical image segmentation that automatically adapts to any dataset. Consistently top-performing on benchmarks like BraTS, KiTS, and AMOS.

Installation

uv pip install nnunetv2

Plan and Preprocess

nnUNetv2_plan_and_preprocess -d DATASET_ID -pl nnUNetPlanner

Train

nnUNetv2_train DATASET_ID CONFIG 0  # CONFIG: 2d, 3d_fullres, 3d_lowres

Inference

nnUNetv2_predict -i INPUT_FOLDER -o OUTPUT_FOLDER -d DATASET_ID -c CONFIG

Python API

from nnunetv2.inference.predict_from_raw_data import nnUNetPredictor

predictor = nnUNetPredictor()
predictor.initialize_from_trained_model_folder("nnUNet_results/DatasetXYZ", "3d_fullres")
predictor.predict_from_files("input_images", "output_segmentations")

Workflow

Prepare dataset in nnUNet format (imagesTr, labelsTr, dataset.json)
Run nnUNetv2_plan_and_preprocess for automatic configuration
Train with nnUNetv2_train
Predict with nnUNetv2_predict or Python API
Ensemble multiple configurations for best accuracy

Frequently asked questions

Nnunet