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    118 repositories

    • nnUNet

      Public
      segmentation
      segmentation
      Python
      •
      Apache License 2.0
      •2.3k•8.1k•337•36•Updated Mar 10, 2026Mar 10, 2026

    • nnActive

      Public
      nnActive -- code, benchmark and results for the largest study of Active Learning for 3D Biomedical Imaging.
      machine-learningcomputer-visionsegmentation
      machine-learningcomputer-visionsegmentationactive-learningnnu-net3d-biomedical
      Python
      •
      Apache License 2.0
      •0•16•0•0•Updated Mar 10, 2026Mar 10, 2026

    • MatchPoint

      Public
      MatchPoint is a translational image registration framework written in C++. It offers a standardized interface to utilize several registration algorithm resource…
      C++
      •3•5•0•0•Updated Mar 10, 2026Mar 10, 2026

    • VoxTell

      Public
      Free-Text Promptable Universal 3D Medical Image Segmentation
      Python
      •
      Apache License 2.0
      •12•159•4•0•Updated Mar 9, 2026Mar 9, 2026

    • batchgeneratorsv2

      Public
      Python
      •
      Apache License 2.0
      •17•28•0•5•Updated Mar 9, 2026Mar 9, 2026

    • deki-smpc

      Public
      Python
      •
      Apache License 2.0
      •0•4•0•0•Updated Mar 9, 2026Mar 9, 2026

    • deki-smpc-server

      Public
      Python
      •
      Apache License 2.0
      •0•3•0•0•Updated Mar 9, 2026Mar 9, 2026

    • mlarray

      Public
      Array format specialized for Machine Learning with Blosc2 backend and standardized metadata.
      Python
      •
      MIT License
      •0•19•0•0•Updated Mar 6, 2026Mar 6, 2026

    • nnInteractive

      Public
      nnInteractive is a framework for 3D interactive segmentation, supporting intuitive prompts like points, scribbles, bounding boxes, and lasso. Trained on 120+ di…
      Python
      •
      Apache License 2.0
      •42•365•17•1•Updated Mar 6, 2026Mar 6, 2026

    • nnLandmark

      Public
      Python
      •
      Apache License 2.0
      •3•21•0•0•Updated Mar 3, 2026Mar 3, 2026

    • acvl_utils

      Public
      Python
      •
      Apache License 2.0
      •4•12•4•2•Updated Mar 2, 2026Mar 2, 2026

    • napari-mlarray

      Public
      A reader/writer Napari plugin for MLArray images
      Python
      •
      MIT License
      •0•1•0•1•Updated Mar 1, 2026Mar 1, 2026

    • napari-voxtell

      Public
      Python
      •
      Apache License 2.0
      •0•18•0•0•Updated Feb 27, 2026Feb 27, 2026

    • napari-nninteractive

      Public
      nnInteractive plugin for Napari - nnInteractive is a framework for 3D interactive segmentation, supporting intuitive prompts like points, scribbles, bounding bo…
      Python
      •
      Apache License 2.0
      •15•107•11•3•Updated Feb 26, 2026Feb 26, 2026

    • MITK-Diffusion

      Public
      MITK Diffusion - Official part of the Medical Imaging Interaction Toolkit
      simulationdicomregistration
      simulationdicomregistrationsegmentationmodellingbrainpeakdiffusion-mritractographydenoising
      C++
      •
      Other
      •16•102•5•0•Updated Feb 24, 2026Feb 24, 2026

    • TractSeg

      Public
      Automatic White Matter Bundle Segmentation
      Python
      •
      Apache License 2.0
      •79•254•61•2•Updated Feb 23, 2026Feb 23, 2026

    • MedVol

      Public
      Python
      •
      Apache License 2.0
      •0•17•0•0•Updated Feb 18, 2026Feb 18, 2026

    • panther

      Public
      Python
      •
      Apache License 2.0
      •2•6•0•0•Updated Feb 17, 2026Feb 17, 2026

    • MeisenMeister

      Public
      Winning Solution of the ODELIA Breast MRI Challenge 2025
      Apache License 2.0
      •0•6•1•0•Updated Feb 16, 2026Feb 16, 2026

    • dynamic-network-architectures

      Public
      Python
      •
      Apache License 2.0
      •58•150•5•4•Updated Feb 9, 2026Feb 9, 2026

    • LesionLocator

      Public
      LesionLocator is a framework for zero-shot lesion segmentation and longitudinal tumor tracking in 3D full-body imaging.
      trackingtumorsegmentation
      trackingtumorsegmentation3dlesion
      Python
      •
      GNU General Public License v3.0
      •9•93•3•0•Updated Feb 3, 2026Feb 3, 2026

    • Longitudinal4DMed

      Public
      Python
      •0•8•0•0•Updated Jan 22, 2026Jan 22, 2026

    • Temporal-Flow-Matching

      Public
      Python
      •0•10•0•0•Updated Jan 16, 2026Jan 16, 2026

    • ToothSeg

      Public
      Python
      •2•32•1•0•Updated Jan 7, 2026Jan 7, 2026

    • napari-data-inspection

      Public
      Data Inspection Plugin, designed to streamline file navigation and enhance the efficiency of data inspection.
      Python
      •
      Apache License 2.0
      •1•14•0•0•Updated Dec 22, 2025Dec 22, 2025

    • ViData

      Public
      A unified Python toolkit for managing, processing, and analyzing 2D and 3D vision data — from raw files to task-aware analytics. Designed to streamline computer…
      Python
      •
      Apache License 2.0
      •0•4•0•0•Updated Dec 22, 2025Dec 22, 2025

    • napari-stream

      Public
      Plugin to send and receive multi-dimensional image data for visualization in Napari over the network.
      Python
      •
      MIT License
      •0•2•0•0•Updated Dec 19, 2025Dec 19, 2025

    • combinedmodalityviewer

      Public
      0•0•0•0•Updated Dec 17, 2025Dec 17, 2025

    • Skeleton-Recall

      Public
      Skeleton Recall Loss for Connectivity Conserving and Resource Efficient Segmentation of Thin Tubular Structures
      Python
      •
      Apache License 2.0
      •11•130•7•1•Updated Dec 8, 2025Dec 8, 2025

    • nnunet-eucaim-docker

      Public
      This repository provides Docker images for running nnUNet inference in a reproducible and containerized environment, tailored for the EUCAIM project.
      Dockerfile
      •
      Apache License 2.0
      •1•0•0•0•Updated Dec 8, 2025Dec 8, 2025