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Leveraging mouse and rat brain atlases to standardize brain-wide mapping in serial sections and cleared intact brain volumes across experiments.
N. J. O’CONNOR1, B. S. EASTWOOD1, P. J. ANGSTMAN1, A. D. LEDUC1, N. D. LIESE1 C. R. GERFEN2, J. R. GLASER1
Presenting author:
Nathan J. O'Connor
Molecular neuroanatomical methods have expanded the ability to map connection activity of neuron subtypes and circuits in behavioral and pathologic models. Analysis of connectivity across mouse and rat brains registered to a digital standardized reference atlas reveals details about the functional organization of brain circuits related to behavior and pathologies and enables comparison of data across animals, experiments, and laboratories.
Our commercial software, NeuroInfo, aligns images of mouse and rat brain sections into whole-brain image volumes and subsequently registers them to the Allen Mouse Brain and Waxholm Rat Brain atlases, respectively. Cleared brain volumes imaged by light-sheet microscopy can also be registered. NeuroInfo accounts for non-orthogonal sectioning and tissue deformities introduced during histological processing to ensure accurate registration. After registration, coordinates of cell populations detected via artificial intelligence are transformed to the corresponding atlas coordinate system and partitioned by brain regions. Anatomical term names are reported alongside persistent unique identifiers to enhance the FAIRness of data endpoints. To further diversify the utility of NeuroInfo, an open specification was published for integrating other standardized digital atlases into this registration technology. We present an example of how this intuitive and comprehensive workflow can be employed to generate rich, interoperable data that efficiently leverages standardized atlases.