nnunet

[ICLR 2024 oral; top 1.2%] Supervised Pre-Trained 3D Models for Medical Image Analysis (9,262 CT volumes + 25 annotated classes)

MOOSE (Multi-organ objective segmentation) a data-centric AI solution that generates multilabel organ segmentations to facilitate systemic TB whole-person research.The pipeline is based on nn-UNet and has the capability to segment 120 unique tissue classes from a whole-body 18F-FDG PET/CT image.

3D Slicer extension for fully-automatic segmentation of CT and CBCT dental volumes.

Segmentation deep learning ALgorithm based on MONai toolbox: single and multi-label segmentation software developed by QIMP team-Vienna.

[CVPR 2025] nnWNet: Rethinking the Use of Transformers in Biomedical Image Segmentation and Calling for a Unified Evaluation Benchmark

3D Slicer nnUNet integration to streamline usage for nnUNet based AI extensions.

MIST: A simple and scalable end-to-end framework for 3D medical imaging segmentation.

cardiAc ultrasound Segmentation & Color-dopplEr dealiasiNg Toolbox (ASCENT)

LION: Lesion Segmentation. Simplified.

LightMIS: Ultra-Lightweight Medical Image Segmentation Without a Stage-Wise Decoder

Fully automated 3D perivascular space (PVS) segmentation tool for T1w and T2w brain MRI.

Playing with SimpleITK and nnU-Net to process data from the CHAOS challenge on Google Colab.

nnUNet benchmarks for The University of California San Francisco Brain Metastases Stereotactic Radiosurgery (UCSF-BMSR) dataset.

Official repository for "Pre- to Post-Contrast Breast MRI Synthesis for Enhanced Tumour Segmentation"

Automated cyst segmentation and counting pipeline for polycystic kidney disease µCT scans, using nnUNet and distance-transform peak detection with genetic algorithm parameter optimization.

Bi-temporal CTP–DWI tissue phenotyping for acute ischemic stroke (IEEE BHI 2026)

This is a repository hosting all models detailed in the article Brain tumour segmentation with incomplete imaging data.

Efficient Deep Learning-based Forward Solvers for Brain Tumor Growth Models

nnUNet benchmarks for The University of California San Francisco Adult Longitudinal Post-Treatment Diffuse Glioma (UCSF-ALPTDG) dataset.