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AtlasAlign

github.com

Align brain microscopy to an atlas, review and export ROIs

Open source

Visit github.comexternal siteGitHub3 starsexternal site

In the makers' words

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. AtlasAlign is an open-source Fiji/ImageJ2 plugin for mouse brain atlas alignment and ROI export.

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