ABBA+BraiAn: New Tools for Whole-Brain Mapping

The innovative pipeline consists of two complementary tools: ABBA (Aligning Big Brains and Atlases), developed by the BIOP, which streamlines the registration of 2D histological sections to 3D reference atlases, and BraiAn (Brain Analysis), developed by the Silva lab, a suite for automated multi-marker analysis and data visualization. ABBA features an intuitive graphical interface that requires no coding skills, supports multiple brain atlases (mouse, rat, zebrafish, human), and handles large imaging datasets efficiently. The BIOP team's expertise in microscopy and image processing was crucial in developing ABBA's advanced features, including multi-resolution image handling and integration with machine learning-based registration tools.

Using these tools, the research team conducted a comprehensive comparison of three widely used immediate-early genes (cFos, Arc, and NPAS4) that serve as markers of neural activity. Their analysis revealed differences in how these markers are distributed across the brain and how they respond to different behavioral experiences. While traditionally used interchangeably, the study reveals that cFos, Arc, and NPAS4 actually provide complementary rather than equivalent information about brain activity, with distinct regional preferences and varying sensitivities to different types of neural stimulation.

The ABBA+BraiAn toolkit addresses limitations of existing brain mapping tools by offering user-friendly interfaces, compatibility with diverse imaging formats, and scalable processing capabilities. BIOP's contribution ensures that researchers worldwide can now perform sophisticated whole-brain analyses without requiring extensive programming expertise or specialized computing resources. While published only recently, this software has already been downloaded by several hundred users worldwide.