Brainreg

Supports numerous anatomical atlases via brainglobe-atlasapi, including the Allen Mouse Brain Atlas at various resolutions, enabling consistent multi-species analysis as highlighted in the documentation.

Incorporates multiple registration backends for robust alignment, evolving from the aMAP pipeline with enhanced algorithms for automated 3D brain image registration.

Offers an optional napari plugin for GUI-based interaction, allowing users to drag-and-drop output directories for immediate visual feedback, as demonstrated in the sample space GIF.

Enables registration of additional image channels to the same coordinate space using the -a flag, facilitating integrated analysis of multi-modal data without manual alignment.