Brainbuilder: a software pipeline for 3D reconstruction of cortical maps from multi-modal 2D data sets

Area of Science:

• Neuroscience
• Computational Biology
• Brain Mapping

Background:

• Mesoscale brain architecture maps are crucial for understanding brain organization.
• Current methods struggle to bridge micro-scale neural data and macro-scale imaging.
• Detailed brain atlases are essential for studying normal and pathological brain function.

Purpose of the Study:

• Introduce BrainBuilder, a novel method and software package.
• Enable reconstruction of 3D cortical maps from 2D serial brain sections.
• Develop a versatile pipeline applicable to different species without donor-specific reference volumes.

Main Methods:

• Utilized 2D post-mortem serial brain sections.
• Processed sections for visualization of multiple biological features (e.g., neurotransmitter receptor binding, cell stains, myelin stains).
• Developed a computational pipeline for 3D reconstruction.

Main Results:

• Successfully reconstructed 3D cortical maps from human and macaque brain data.
• Demonstrated the ability to visualize diverse biological features within the reconstructed maps.
• Validated the pipeline's applicability across species.

Conclusions:

• BrainBuilder provides a robust method for creating mesoscale 3D brain maps.
• The software facilitates the development of advanced 3D brain atlases.
• This approach enhances the study of brain architecture and function.