AtlasAlign

What it does

Open-source image alignment and brain atlas registration for Fiji / ImageJ2. Review mouse brain microscopy against Allen CCFv3, select anatomical ROIs, and export crops and masks. Supports resumable batch review. - Release AtlasAlign Lite 0.1.0-beta.3 — multichannel review and saved sessions · meghamsh738/atlasalign

AtlasAlign beta.3 adds multichannel/composite viewing, pinned C/Z/T registration, selected-channel source-plane exports, complete saved review sessions and batch checkpoints, and clearer manual alignment controls. The source image stays read-only. Anatomical alignment and ROI boundaries still require researcher review. Install the Fiji add-on ZIP using the included installation guide; the source ZIP contains a clean, history-free source snapshot. Java 17+ and Fiji/ImageJ2 are required. Manual alignment does not require Python. Validation: beta.3 Windows, macOS and Linux CI passed. The local full suite and packaged runtime/isolated Fiji command-discovery/source-integrity smokes passed. The…from github.com

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