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