Repositories list

• 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 Dec 21, 2025Dec 21, 2025

• axondeepseg

  Public
  Axon/Myelin segmentation using Deep Learning

  machine-learningdeep-learningsegmentation+ 8convolutional-neural-networkselectron-microscopyaxonmicroscopymyelinspinalcordhistology+ 1

  Python

  •

  MIT License

  •31•124•45•1•Updated Dec 12, 2025Dec 12, 2025

• eval-object-det

  Public
  Pipeline to compare semantic segmentation model output against manual cell counts. We compute Precision, Recall and F-Score

  Python

  •0•0•0•0•Updated Nov 14, 2025Nov 14, 2025

• data-testing

  Public
  Images and files used for software testing (unit and integration tests).

  MIT License

  •0•0•0•0•Updated Nov 5, 2025Nov 5, 2025

• 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

• doc-figures

  Public
  Repository that contains most figures for axondeepseg documentation.

  MIT License

  •0•0•0•0•Updated Sep 17, 2025Sep 17, 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

  •2•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•2•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

  •48•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