Quantitative Brain-Wide Neuronal Mapping Through Three-Dimensional Reconstruction and Atlas Alignment of Serial Tissue Sections
Background: Understanding neural circuits requires whole-brain mapping of specific neuronal connections within a standardized framework. Although modern genetic and viral tools allow precise labeling of neurons, integrating these data into complete brain reconstructions using conventional histological methods has been difficult.
Hypothesis: This study hypothesized that whole mouse brain reconstructions from conventionally sectioned and processed tissue can be accurately registered to a common reference atlas, enabling quantitative analysis of labeled neurons and axons throughout the brain.
Methods: The authors sectioned mouse brains labeled via modified rabies transsynaptic tracing and immunohistochemistry, imaged them using a fluorescence microscope equipped with Neurolucida software, and reconstructed serial coronal sections into a three-dimensional brain volume using BrainMaker software. Labeled cells were automatically detected through a Laplacian of Gaussian–based algorithm implemented in NeuroInfo, and whole-brain images were registered to the CCF v3 through a multistage registration pipeline.
Results: Registration accuracy tests showed mean landmark errors of approximately 63 µm in three-dimensional space and about 21 µm within imaging planes. Quantitative analysis of registered datasets generated spreadsheets of cell counts across atlas-defined structures, allowing comparisons between cases. Reconstructions revealed distinct distributions of neurons projecting to different cortical areas, demonstrating consistent alignment and reproducibility across brains.
Conclusions: This study established that whole-brain reconstructions from standard histological sections can be precisely registered to a reference atlas, enabling automated detection and quantitative comparison of labeled neurons across experiments. This approach facilitates high-resolution mapping of brain-wide connectivity using widely available laboratory techniques.
Eastwood BS, Hooks BM, Paletzki RF, O’Connor NJ, Glaser JR, Gerfen CR. Whole mouse brain reconstruction and registration to a reference atlas with standard histochemical processing of coronal sections. J Comp Neurol 2019;527(13):2170-2178. doi: 10.1002/cne.24602.
