Tissue-Cleared Wild-Type P0 Whole Mouse Brains Imaged by Lightsheet Microscopy

3D imaging of intact, tissue-cleared mouse brains enables cellular quantification across the whole brain for applications ranging from tracing normal neurodevelopment to disease models. To facilitate comparison across mouse models, 3D atlases and wild-type controls are required for the appropriate strain, sex, and age. We have generated 3D reconstructions of the Allen Developing Mouse Brain Atlas to fill in missing sections, correct artifacts, and optimize alignment with the underlying histology. To validate these atlases, we generated 15 volumetric images of C57BL/6J wild-type mouse pup brains at postnatal day 0 (10 male, 5 female) using lightsheet microscopy. Mouse brains were cleared using the CUBIC clearing technique given its balance of transparency, morphological preservation, and ease of handling. SYTO 16 nuclear dye labeled cells throughout each brain, while 5x objective magnification provided cellular resolution. We registered our 3D reconstructed E18.5 atlas [(DOI: 10.25493/X4ZT-ARE)](https://doi.org/10.25493%2FX4ZT-ARE) to each of these brains for quantitative cellular analysis by region. These whole-brain images can be reused for further evaluation of 3D atlases, characterization of wild-type neuroanatomy, or additional controls for mouse-based brain-wide neurological studies.