A Fiji-based platform for whole-brain reconstruction and analysis. BrainJ assembles serial tissue sections from slide scanners and confocal microscopes into reconstructed brains, registers them to a common coordinate framework, and supports cell mapping and mesoscale projection analysis.
BrainJ was developed at the Zuckerman Mind Brain Behavior Institute at Columbia University to make whole-brain reconstruction and analysis accessible to bench scientists working with confocal microscopes and slide scanners. It integrates open-source tools, including Ilastik for machine-learning pixel classification, into a single Fiji-based workflow that minimizes manual intervention and supports high-throughput processing.
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