2D structural annotation and 3D reconstruction of the whole brain of Alligator sinensis

Abstract The Chinese alligator ( Alligator sinensis ) is a small crocodilian endemic to China; current neuroanatomical knowledge of its whole brain remains limited. In the present study, we combined the Micro‐Optical Sectioning Tomography system with Imaris, CorelDRAW, and MATLAB software to generate a histological atlas of the entire Chinese alligator brain and reconstruct its 3D digital brain model. Results showed that the whole brain of the Chinese alligator is anatomically partitioned into eight major compartments: olfactory bulb (OB), olfactory tract (OTr), telencephalon (Tel), diencephalon (Dien), mesencephalon (Mes), cerebellum (Cer), pituitary gland (PG), and medulla oblongata (MO). Most distinguishable cytoarchitectonic structures reside within the Tel, Dien, and Mes. The main OB exhibits a finely laminated cytoarchitecture, whereas an accessory olfactory bulb (AOB) is absent. Collectively, the Tel and Dien occupy approximately one‐third of the total brain volume. The mesencephalic tectum displays distinct laminar organization, with the corpora quadrigemina (CQ) differentiated into superior and inferior colliculi. A total of 116 discrete brain structures were annotated in this atlas. We unambiguously identified a pineal body (PB) in the Chinese alligator, substantially expanding the fundamental neurohistological dataset of crocodilian brains. This work establishes a foundational morphological template for reptilian nervous system research and provides critical comparative anatomical references for evolutionary neurobiology across all vertebrate lineages.