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

## TL;DR

BrainBuilder is a new software tool that creates 3D brain maps from 2D slices, helping researchers study brain structure at a detailed mesoscale level.

## Contribution

BrainBuilder introduces a novel pipeline for 3D cortical map reconstruction from multi-modal 2D brain data without requiring a reference volume.

## Key findings

- BrainBuilder successfully reconstructs 3D maps from human and macaque brain sections showing neurotransmitter receptors and myelin staining.
- The pipeline supports species-agnostic reconstruction, making it useful for diverse brain studies.
- It provides a foundation for developing future mesoscale 3D brain atlases.

## Abstract

Mesoscale maps of brain architecture are important tools for characterizing the chemo- and cytoarchitectonic organization of the brain. These maps are essential for advancing our understanding of normal and pathologic brain function because they provide a bridge between neuron-level micro-scale imagining and macro-level population brain imaging. Here we introduce a method and software package called BrainBuilder for reconstructing 3-dimensional cortical maps from data sets of 2-dimensional post-mortem serial brain sections processed for the visualization of multiple different biological features. This pipeline can be applied to the brains from different species, without the strict need for a corresponding reference volume from the brain donor. As a proof of principle, we reconstruct data showing the distribution of multiple neurotransmitter receptor binding sites, and cell and myelin stained sections in the human and macaque brain. We show that BrainBuilder can serve as the basis for the development of future mesoscale 3D atlases.

BrainBuilder is a new tool for reconstructing 3D cortical maps from 2D post-mortem brain sections, enabling mesoscale mapping of chemo- and cytoarchitecture for sparse, multi-modal data sets.