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    32 repositories

    • model_seg_unmyelinated_tem

      Public
      Model for unmyelinated axon segmentation in TEM images, based on nnUNet
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 16, 2025Oct 16, 2025

    • axondeepseg

      Public
      Axon/Myelin segmentation using Deep Learning
      machine-learningdeep-learningsegmentationconvolutional-neural-networkselectron-microscopyaxonmicroscopymyelinspinalcordhistology
      Python
      •
      MIT License
      •31•122•44•0•Updated Oct 16, 2025Oct 16, 2025

    • data-testing

      Public
      Images and files used for software testing (unit and integration tests).
      MIT License
      •0•0•0•0•Updated Oct 15, 2025Oct 15, 2025

    • doc-figures

      Public
      Repository that contains most figures for axondeepseg documentation.
      MIT License
      •0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • ASTIH

      Public
      Axon Segmentation Training Initiative for Histology: A collection of datasets for axon and myelin segmentation in microscopy images.
      Python
      •
      MIT License
      •0•1•2•0•Updated Jul 29, 2025Jul 29, 2025

    • model-seg-human-brain-cars

      Public
      Axon and myelin segmentation model in histology images to quantify myelination in the human brain. Training data was acquired in the uncinate fasciculus using CARS microscopy.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • model_seg_killifish

      Public
      Myelinated & Unmyelinated Axon Segmentation in Teleost Killifish TEM Images
      Python
      •0•0•0•0•Updated May 26, 2025May 26, 2025

    • data_axondeepseg_srf_testing

      Public
      Testing set of https://dandiarchive.org/dandiset/001350/0.250511.1527
      MIT License
      •0•0•0•0•Updated May 13, 2025May 13, 2025

    • data_axondeepseg_sem

      Public
      SEM dataset for AxonDeepSeg. Example dataset containing scanning electron microscopy (SEM) data to illustrate BIDS convention.
      MIT License
      •0•2•3•1•Updated May 9, 2025May 9, 2025

    • data_ci

      Public
      0•0•0•0•Updated Apr 29, 2025Apr 29, 2025

    • seg_ci

      Public
      Shell
      •0•0•0•0•Updated Apr 29, 2025Apr 29, 2025

    • axon-detection

      Public
      Exploration of object detection applied to the AxonDeepSeg project
      Jupyter Notebook
      •1•1•8•1•Updated Mar 26, 2025Mar 26, 2025

    • nn-axondeepseg

      Public
      1-class and 2-class segmentation of axon/myelin using nnunetv2
      Python
      •0•1•5•0•Updated Sep 26, 2024Sep 26, 2024

    • AxonDeepSynth

      Public
      AxonDeepSynth is a framework leveraging the SynDiff model for unsupervised image translation, designed to enhance segmentation model performance across different imaging modalities in out-of-distribution (OOD) scenarios. Link to the paper is: https://www.arxiv.org/abs/2412.02858
      Python
      •
      Other
      •44•1•0•1•Updated Jun 24, 2024Jun 24, 2024

    • model_seg_generalist

      Public
      Axon and myelin segmentation model trained on all ADS datasets. Works across contrasts and resolutions.
      Python
      •0•2•2•0•Updated Apr 30, 2024Apr 30, 2024

    • model_seg_nerve

      Public
      Nerve area segmentation for axon density estimation in BF images
      Python
      •0•0•0•0•Updated Apr 18, 2024Apr 18, 2024

    • awesome-histology-segmentation

      Public
      Creative Commons Zero v1.0 Universal
      •0•1•1•0•Updated Apr 17, 2024Apr 17, 2024

    • default-wakehealth-model

      Public
      AxonDeepSeg default Wakehealth model and testing image
      Python
      •
      MIT License
      •0•0•1•0•Updated Apr 8, 2024Apr 8, 2024

    • default-BF-model

      Public
      AxonDeepSeg default BF model
      Python
      •
      MIT License
      •0•0•1•0•Updated Apr 5, 2024Apr 5, 2024

    • model_seg_rabbit_axon-myelin_bf

      Public
      Standard 2-class segmentation model for ADS trained on rabbit samples (Virginia Commonwealth University)
      Python
      •1•0•1•0•Updated Apr 5, 2024Apr 5, 2024

    • default-TEM-model

      Public
      AxonDeepSeg default TEM model and testing image
      Python
      •
      MIT License
      •0•0•3•0•Updated Apr 3, 2024Apr 3, 2024

    • default-CARS-model

      Public
      AxonDeepSeg default CARS model
      Python
      •
      MIT License
      •0•0•1•0•Updated Apr 3, 2024Apr 3, 2024

    • default-SEM-model

      Public
      AxonDeepSeg default SEM model and testing image
      Python
      •
      MIT License
      •0•0•1•1•Updated Apr 3, 2024Apr 3, 2024

    • model_postprocess_touching_myelin

      Public
      Training nnUNet v2 for Detecting Boundaries Between Touching Myelinated Axon
      Python
      •
      MIT License
      •0•0•2•0•Updated Mar 13, 2024Mar 13, 2024

    • model_seg_human_axon-myelin_bf

      Public
      AxonDeepSeg model trained on Toluidine Blue stained BF optical microscopy samples
      0•0•0•0•Updated Feb 13, 2024Feb 13, 2024

    • sam_myelin_seg_TEM

      Public
      Axon and Myelin segmentation using FAIR's Segment-Anything-Model (SAM)
      Python
      •
      MIT License
      •0•0•6•0•Updated Nov 16, 2023Nov 16, 2023

    • synthetic_image_gen_model

      Public
      This repository is following the internship idea to generate synthetic data using GANS.
      Python
      •0•0•1•1•Updated Aug 18, 2023Aug 18, 2023

    • napari-plugin

      Public archive
      A (work in progress) plugin for napari that implements the AxonDeepSeg tools
      Python
      •0•0•3•0•Updated Mar 2, 2023Mar 2, 2023

    • ometiff-tests

      Public
      Files used to test OME-TIFF images for BIDS-microscopy
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Jan 6, 2022Jan 6, 2022

    • model_seg_rat_axon-myelin_sem

      Public
      [For Development] Early SEM IVADOMED model.
      0•0•0•0•Updated Aug 6, 2021Aug 6, 2021