Pinned Repositories
awesome-histology-segmentation
axon-detection
Exploration of object detection applied to the AxonDeepSeg project
axondeepseg
Axon/Myelin segmentation using Deep Learning
data_axondeepseg_sem
SEM dataset for AxonDeepSeg. Example dataset containing scanning electron microscopy (SEM) data to illustrate BIDS convention.
model-seg-human-brain-cars
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.
model_seg_generalist
Axon and myelin segmentation model trained on all ADS datasets. Works across contrasts and resolutions.
model_seg_unmyelinated_tem
Model for unmyelinated axon segmentation in TEM images, based on nnUNet
nn-axondeepseg
1-class and 2-class segmentation of axon/myelin using nnunetv2
ometiff-tests
Files used to test OME-TIFF images for BIDS-microscopy
synthetic_image_gen_model
This repository is following the internship idea to generate synthetic data using GANS.
AxonDeepSeg's Repositories
axondeepseg/axondeepseg
Axon/Myelin segmentation using Deep Learning
axondeepseg/awesome-histology-segmentation
axondeepseg/data_axondeepseg_sem
SEM dataset for AxonDeepSeg. Example dataset containing scanning electron microscopy (SEM) data to illustrate BIDS convention.
axondeepseg/model_seg_generalist
Axon and myelin segmentation model trained on all ADS datasets. Works across contrasts and resolutions.
axondeepseg/model_seg_unmyelinated_tem
Model for unmyelinated axon segmentation in TEM images, based on nnUNet
axondeepseg/nn-axondeepseg
1-class and 2-class segmentation of axon/myelin using nnunetv2
axondeepseg/axon-detection
Exploration of object detection applied to the AxonDeepSeg project
axondeepseg/AxonDeepSynth
Official PyTorch implementation of SynDiff described in the paper (https://arxiv.org/abs/2207.08208).
axondeepseg/data-example
Example dataset used in documentation
axondeepseg/data-testing
Images and files used for software testing (unit and integration tests).
axondeepseg/default-BF-model
AxonDeepSeg default BF model
axondeepseg/default-CARS-model
AxonDeepSeg default CARS model
axondeepseg/default-SEM-model
AxonDeepSeg default SEM model and testing image
axondeepseg/default-TEM-model
AxonDeepSeg default TEM model and testing image
axondeepseg/doc-figures
Repository that contains most figures for axondeepseg documentation.
axondeepseg/model-seg-human-brain-cars
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.
axondeepseg/model-seg-pns-bf
OM model that works at a resolution of 0.1 micrometer per pixel
axondeepseg/model_seg_human_axon-myelin_bf
AxonDeepSeg model trained on Toluidine Blue stained BF optical microscopy samples
axondeepseg/model_seg_nerve
Nerve area segmentation for axon density estimation in BF images
axondeepseg/model_seg_rabbit_axon-myelin_bf
Standard 2-class segmentation model for ADS trained on rabbit samples (Virginia Commonwealth University)
axondeepseg/model_seg_rat_axon-myelin_sem
[For Development] Early SEM IVADOMED model.
axondeepseg/napari-plugin
A (work in progress) plugin for napari that implements the AxonDeepSeg tools
axondeepseg/ometiff-tests
Files used to test OME-TIFF images for BIDS-microscopy
axondeepseg/sam_myelin_seg_TEM
Axon and Myelin segmentation using FAIR's Segment-Anything-Model (SAM)
axondeepseg/synthetic_image_gen_model
This repository is following the internship idea to generate synthetic data using GANS.
axondeepseg/data_ci
axondeepseg/default-wakehealth-model
AxonDeepSeg default Wakehealth model and testing image
axondeepseg/model_postprocess_touching_myelin
Training nnUNet v2 for Detecting Boundaries Between Touching Myelinated Axon
axondeepseg/seg_ci