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@axondeepseg AxonDeepSeg

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    29 repositories

    • axondeepseg

      Public
      Axon/Myelin segmentation using Deep Learning
      machine-learningsegmentationelectron-microscopymicroscopymyelinspinalcordhistologyneuropolydeep-learningconvolutional-neural-networks
      Python
      •
      MIT License
      •32•116•31•6•Updated Dec 20, 2024Dec 20, 2024

    • axon-detection

      Public
      Exploration of object detection applied to the AxonDeepSeg project
      Jupyter Notebook
      •0•1•8•0•Updated Dec 20, 2024Dec 20, 2024

    • data-testing

      Public
      Images and files used for software testing (unit and integration tests).
      MIT License
      •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

    • doc-figures

      Public
      Repository that contains most figures for axondeepseg documentation.
      MIT License
      •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

    • model_seg_unmyelinated_tem

      Public
      Model for unmyelinated axon segmentation in TEM images, based on nnUNet
      Python
      •
      MIT License
      •0•1•0•0•Updated Dec 5, 2024Dec 5, 2024

    • 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 Nov 6, 2024Nov 6, 2024

    • seg_ci

      Public
      Shell
      •0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

    • 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

    • data_ci

      Public
      0•0•0•0•Updated Sep 20, 2024Sep 20, 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
      •37•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•1•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

    • 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•0•Updated Nov 30, 2021Nov 30, 2021

    • model_seg_rat_axon-myelin_sem

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

    • data-example

      Public
      Example dataset used in documentation
      MIT License
      •1•0•0•0•Updated Jun 21, 2021Jun 21, 2021

    • model-seg-pns-bf

      Public
      OM model that works at a resolution of 0.1 micrometer per pixel
      MIT License
      •0•0•0•0•Updated Jun 15, 2021Jun 15, 2021