Atlas Alignment

The goal of this project is to facilitate the registration of gene expression images to a reference (Nissl) atlas.

Contents:

• Installation
  • Python Requirements
  • External Dependencies
  • Installation from PyPI
  • Installation from source
  • Development installation
  • Generating documentation
• Image Registration 101
• Building Blocks
  • Displacement field
  • Image warping
  • Annotation warping
  • Inversion
  • Composition
  • Resizing
  • Anchoring
• Datasets
  • Nissl volume
  • Annotation volume
  • Manual registration
  • Dummy
• Intensity Based Registration
  • ANTsPy
• Labeling tool
  • Launching
  • Interface
  • FAQ
• Deep Learning - Generating a dataset
  • Geometric augmentations
  • Intensity augmentations
  • Putting things together
  • Example
• Deep Learning - Training
  • Training data
  • Custom Layers
  • Architecture
  • Loss function
  • Saving model
• Deep Learning - Inference
  • Loading model
  • Merging
  • Forward pass
• Metrics and Evaluation
  • Image Similarity Metrics
  • Displacement Field Metrics
  • Segmentation Metrics
  • Compute Many Metrics at Once
• 3D Interpolation
  • CoronalInterpolator

API Reference

• atlalign
  • atlalign package

Indices and tables

• Index

• Module Index

• Search Page

Source

index.rst