Development of brain templates for whole brain atlases

摘要

In neuroscience, Brain template images and annotation atlases are key to analyzing whole brain microscopy images in acommon coordinate framework (CCF) and sharing of anatomical data among neuroscientists. Mapping individual animalspecimen brain to a common space allows neuroscientists compare and utilize data from experiments done on othermodalities or markers. With the advent of new clearing and novel light microscopy techniques, large number of samplesare imaged in these unique combinations of clearing and microscopy that the experimenter deems best to bring out thebest signal-to-noise ratio for their biological data. This paper describes our framework that each such experimenter tocreate a template brain registered with the Allen CCF for their unique combination. Further, we demonstrate the abilityof the framework to create a template brain for an enhanced delipidation protocol called UClear [Unpublished] andimaged using LaVision BioTech Ultramicroscope Ⅱ. The cleared brains were imaged in dibenzyl ether (DBE) under488-nm illumination conditions that allowed the visualization of major brain regions based on intrinsic tissueautofluorescence. As contrast in these images differs from brains imaged by serial two-photon tomography used togenerate the CCF space of the Allen Mouse Brain Atlas, we developed a new CCF brain template for processing andanalysis of the UClear brains. This brain template generation method can make the registration pipeline agnostic to thetissue clearing and imaging protocol.