AtlasAlign is an open-source Fiji/ImageJ2 plugin for mouse brain atlas alignment and ROI export. Beta.3 adds multichannel and composite viewing, registration pinned to C/Z/T, selected-plane exports, and saved review sessions. Refine alignment, edit anatomical ROIs, and export crops and masks in original image coordinates. Resume individual or batch reviews. Source images stay read-only; researchers review and accept the anatomy. Demo frames show the earlier interface.
