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    • PyTorch Connectomics: segmentation toolbox for EM connectomics
      Python
      MIT License
      8619100Updated Apr 17, 2026Apr 17, 2026
    • Fill holes in binary 2D & 3D images fast.
      C++
      GNU Lesser General Public License v3.0
      5000Updated Apr 17, 2026Apr 17, 2026
    • JavaScript
      51244Updated Apr 16, 2026Apr 16, 2026
    • MedNeXt

      Public
      [MICCAI 2023] MedNeXt is a fully ConvNeXt architecture for 3D medical image segmentation.
      Python
      Apache License 2.0
      62000Updated Apr 3, 2026Apr 3, 2026
    • waterz

      Public
      Simple watershed and agglomeration library for affinity graphs.
      Python
      28000Updated Mar 31, 2026Mar 31, 2026
    • abiss

      Public
      Affinity based image segmentation system
      C++
      GNU General Public License v3.0
      4000Updated Mar 30, 2026Mar 30, 2026
    • em_util

      Public
      toolbox utility functions
      Python
      MIT License
      41000Updated Mar 9, 2026Mar 9, 2026
    • em_erl

      Public
      Evaluation script for expected run length (ERL)
      Python
      MIT License
      1210Updated Mar 7, 2026Mar 7, 2026
    • Python
      1000Updated Jan 22, 2026Jan 22, 2026
    • SynAnno

      Public
      A tool for proofreading and refining synaptic polarity annotations in electron microscopy volumes.
      Jupyter Notebook
      MIT License
      11031Updated Oct 13, 2025Oct 13, 2025
    • MitoEM2.0

      Public
      0000Updated Aug 21, 2025Aug 21, 2025
    • VesiclePy

      Public
      HTML
      MIT License
      2600Updated Jul 31, 2025Jul 31, 2025
    • Python
      MIT License
      0000Updated Jul 9, 2025Jul 9, 2025
    • Python
      2000Updated Dec 3, 2024Dec 3, 2024
    • em_agglo

      Public
      Python
      MIT License
      0000Updated Oct 22, 2024Oct 22, 2024
    • em_seg

      Public
      EM segment library and tutorials
      Python
      0100Updated Aug 6, 2024Aug 6, 2024
    • Python
      MIT License
      0000Updated Apr 30, 2024Apr 30, 2024
    • utility code for AxonEM challenge
      Python
      MIT License
      1800Updated Jan 4, 2024Jan 4, 2024
    • tutorial

      Public
      0000Updated Dec 13, 2023Dec 13, 2023
    • Evaluation code for BvEM challenge
      Jupyter Notebook
      MIT License
      0000Updated Nov 29, 2023Nov 29, 2023
    • scripts to download datasets
      MIT License
      0000Updated Nov 8, 2023Nov 8, 2023
    • datasets

      Public
      CSS
      1000Updated Aug 9, 2023Aug 9, 2023
    • C++
      22000Updated Feb 15, 2023Feb 15, 2023
    • WASPSYN23

      Public
      An Out-of-Domain Synapse Detection Challenge for Microwasp Brain Connectomes
      HTML
      0000Updated Jan 26, 2023Jan 26, 2023
    • Grand Challenge evaluation repo for SNEMI3D
      Python
      0200Updated Oct 11, 2022Oct 11, 2022
    • starter code for mitoEM ISBI2021 Challenge
      Jupyter Notebook
      MIT License
      0700Updated Jul 29, 2022Jul 29, 2022
    • Python
      7000Updated Feb 22, 2021Feb 22, 2021
    • Python scripts to read and write the CREMI hdf5 file format.
      Python
      25000Updated Aug 24, 2018Aug 24, 2018
    • Cython functions for fast watersheds and segmentation metrics
      C++
      9000Updated Jul 5, 2016Jul 5, 2016
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