An awesome list of histology segmentation tools.
Inspired by awesome-php.
- Axon/Myelin
- AxonDeepSeg Axon/Myelin segmentation using Deep Learning, with added morphological metric tools and Napari GUI plugin.
- AxonSeg Segment axon and myelin from microscopy data.
- hifuku Morphometric analysis of sural nerve biopsies.
- AxonSeg-3D-CNN Analyze the 3D white matter microstructure using 3D CNNs in 3D synchrotron X-ray nano-holotomography
- g-ratio selection Automatic segmentation and selection of clinically relevant axon and myelin
- large-scale axon segmentation Mapping the MRI-visible, effective radius (r_eff) by combining high-resolution, large-scale light microscopy (lsLM) with deep learning.
- DeepACSON Segments myelin and axon for 3D histology
- Axon-only
- D-LMBmap Automated axon segmentation from small cubes to whole brain.
- autoballs Pipeline for analysis of ex vivo axons explants segmentation and morphological analysis.
- ssl for axons Self-Supervised Feature Extraction for 3D Axon Segmentation.
- gACSON Software for visualization, processing and analysis of three-dimensional electron microscopy images.
- AxoNet A Deep Learning-Based Tool for Morphometric Analysis of Retinal Ganglion Cell Axons
- AxonEM Challenge 3D Axon Instance Segmentation of Brain Cortical Regions
- Myelin-only
- MyelinDeepContourSegmentation Instance segmentation model to individualize each myelin sheath.
- Segmentation-of-myelin-in-electron-microscopy-images Solves the problem of small connection in image segmentation.
- General
- CDeep3M2 Plug-and-Play deep learning for image segmentation of large-scale microscopy data
- [ANMAF]https://github.com/stephenbaek/ANMAF) Automated Neuronal Morphology Analysis Framework using Convolutional Neural Networks
- CellWalker Segmentation tools for three-dimensional images
- [Segment Anything for Microscopy] Napari segmentation tool for interactively segmenting any histology objects.
- Axon/Myelin
- Axon-only
- axonSegmentation Semi-automated instance annotation of 3D microscopy images. Based on curvilinear filters followed by modified search.
- Myelin-only
- MyelTracer A semi-Aatomated software for myelin g-ratio quantification.
- Deep-Active-Learning-for-Myelin-Segmentation-on-Histology-Data Uncertainty measure by Monte Carlo samples, using Dropout regularization scheme