An awesome list of histology segmentation tools.

Inspired by awesome-php.

• Awesome Histology Segmentation
  • Fully-automated
  • Semi-automated
  • Manual

• 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
  • AimSeg Segmentation of three axonal components (axoplasm, inner cytoplasmic tongue and myelin) on TEM images using Fiji and ilastik.
  • RaW-seg Random walker (RaW) segmentations of myelinated axons in 3d electron microscopy (EM) data
• 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