Morphology-Classification

MorphoClass is a python package that provides machine learning based tools for morphology type recognition of neuron reconstructions.

Solutions for both supervised and unsupervised learning are provided, as well as an ecosystem for data handling, transformation, and augmentation, training, visualisation, and tools for explainable AI. The main focus of machine learning models is on graph neural networks, but other solution can also benefit from the provided ecosystem.

Contents

• Installation
  • Basic
  • Check the Installation
  • Development
  • Why an Installation Script?
  • DeepWalk and CleanLab
• Project Tree
• Docker
• Building the Documentation
• CLI
  • Overview
  • Subcommands
• DVC
  • Data pre-processing
  • Feature extraction
  • Training
  • Evaluation
  • Outdated stages
  • DVC Cache
• Data
  • Loading Datasets
  • Data Objects
  • Filters
  • Transforms
  • Persistence Images and Diagrams
• Models - GNNs
  • Loading Data
  • Training
  • Evaluating
• Models - CNNs
  • Loading Data
  • Training
  • Evaluating
• Models - PersLay
  • Data Loading
  • Training
  • Evaluation
• Custom Models and Layers
  • Layers
  • Models
  • Example
• Example - Design a GNN
  • Data
  • The Net
  • The Training Loop
  • Visualizing Results

API

• morphoclass
  • Subpackages
  • Submodules
  • Module contents

Indices and tables

• Index

• Module Index

• Search Page