A Scanning Electron Microscopy-Compatible Optical Imaging Method for Mesoscopic All-Cell Brain Mapping

Understanding the structural and functional relationships within complex neural networks in the brain requires the construction of brain atlases that possess both a broad field of view and subcellular resolution. However, current optical and electron microscopy imaging methods each have limitations, making it difficult to image all cells within a single specimen. This protocol introduces an imaging technique called Optical Multilayer Interference Tomography (OMLIT), which enables indiscriminate optical imaging of all cells in brain specimens made following electron microscopy sample preparation, thereby reconstructing a complete brain atlas of all neural cells. In addition, OMLIT imaging can be seamlessly integrated with the imaging workflow of automated tape-collecting ultramicrotomy scanning electron microscopy (ATUM-SEM). This allows researchers to obtain mesoscale structural information of cells prior to electron microscopy imaging, facilitating the precise selection of regions of interest and significantly reducing the area and data volume required for high-resolution electron microscopy (EM) imaging. We validated the accuracy and compatibility of this method in actual samples from the adult mouse cerebral cortex, demonstrating its broad application prospects in multi-scale brain atlas construction.