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@PytorchConnectomics Pytorch Connectomics

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    29 repositories

    • pytorch_connectomics

      Public
      PyTorch Connectomics: segmentation toolbox for EM connectomics
      computer-visiondeep-learningneuroscience
      computer-visiondeep-learningneurosciencepytorchsegmentationconnectomicsmicroscopybiomedical-image-processing
      Python
      •
      MIT License
      •86•191•0•0•Updated Apr 17, 2026Apr 17, 2026

    • fill_voids

      Public
      Fill holes in binary 2D & 3D images fast.
      C++
      •
      GNU Lesser General Public License v3.0
      •5•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • pytc-client

      Public
      JavaScript
      •5•1•24•4•Updated 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
      •62•0•0•0•Updated Apr 3, 2026Apr 3, 2026

    • waterz

      Public
      Simple watershed and agglomeration library for affinity graphs.
      Python
      •28•0•0•0•Updated Mar 31, 2026Mar 31, 2026

    • abiss

      Public
      Affinity based image segmentation system
      C++
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Mar 30, 2026Mar 30, 2026

    • em_util

      Public
      toolbox utility functions
      Python
      •
      MIT License
      •4•10•0•0•Updated Mar 9, 2026Mar 9, 2026

    • em_erl

      Public
      Evaluation script for expected run length (ERL)
      Python
      •
      MIT License
      •1•2•1•0•Updated Mar 7, 2026Mar 7, 2026

    • fiberpipeline

      Public
      Python
      •1•0•0•0•Updated Jan 22, 2026Jan 22, 2026

    • SynAnno

      Public
      A tool for proofreading and refining synaptic polarity annotations in electron microscopy volumes.
      Jupyter Notebook
      •
      MIT License
      •1•10•3•1•Updated Oct 13, 2025Oct 13, 2025

    • MitoEM2.0

      Public
      0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

    • VesiclePy

      Public
      HTML
      •
      MIT License
      •2•6•0•0•Updated Jul 31, 2025Jul 31, 2025

    • pytc-deploy

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 9, 2025Jul 9, 2025

    • Vessel2Graph

      Public
      Python
      •2•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • em_agglo

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • em_seg

      Public
      EM segment library and tutorials
      Python
      •0•1•0•0•Updated Aug 6, 2024Aug 6, 2024

    • Anatomics-MLT

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 30, 2024Apr 30, 2024

    • AxonEM-challenge

      Public
      utility code for AxonEM challenge
      Python
      •
      MIT License
      •1•8•0•0•Updated Jan 4, 2024Jan 4, 2024

    • tutorial

      Public
      0•0•0•0•Updated Dec 13, 2023Dec 13, 2023

    • BvEM-challenge

      Public
      Evaluation code for BvEM challenge
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 29, 2023Nov 29, 2023

    • datasets-download

      Public
      scripts to download datasets
      MIT License
      •0•0•0•0•Updated Nov 8, 2023Nov 8, 2023

    • datasets

      Public
      CSS
      •1•0•0•0•Updated Aug 9, 2023Aug 9, 2023

    • L1-Skeleton

      Public
      C++
      •22•0•0•0•Updated Feb 15, 2023Feb 15, 2023

    • WASPSYN23

      Public
      An Out-of-Domain Synapse Detection Challenge for Microwasp Brain Connectomes
      HTML
      •0•0•0•0•Updated Jan 26, 2023Jan 26, 2023

    • snemi3d-gc

      Public
      Grand Challenge evaluation repo for SNEMI3D
      Python
      •0•2•0•0•Updated Oct 11, 2022Oct 11, 2022

    • MitoEM-challenge

      Public
      starter code for mitoEM ISBI2021 Challenge
      Jupyter Notebook
      •
      MIT License
      •0•7•0•0•Updated Jul 29, 2022Jul 29, 2022

    • funlib.evaluate

      Public
      Python
      •7•0•0•0•Updated Feb 22, 2021Feb 22, 2021

    • cremi_python

      Public
      Python scripts to read and write the CREMI hdf5 file format.
      Python
      •25•0•0•0•Updated Aug 24, 2018Aug 24, 2018

    • zwatershed

      Public
      Cython functions for fast watersheds and segmentation metrics
      C++
      •9•0•0•0•Updated Jul 5, 2016Jul 5, 2016
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