Mosaic microtomography of a full mouse brain with sub-micron pixel size

Mammalian brains are extremely complex: a mouse brain contains one hundred million neurons. Mapping an entire brain's three-dimensional cytoarchitecture from the nano- to centimeter-scale is a monumental challenge. For standard microtomography with sub-mu m pixel size, reconstructed volume is limited to about a few mm(3). For full brain mapping, even for the mouse brain with volume of 450mm(3), the field-of-view must be significantly increased in all three dimensions. We demonstrate mosaic tiling to extend imaged volume by 400x and a dedicated pipeline to process these tera-voxel sized datasets. Here, an entire mouse brain was imaged with 0:65 mu m-wide voxels. The datasets, which are 6 TB in size at 16-bit depth, contain a wealth of microanatomical information but present challenges for registration and segmentation.

Automated summary

This article introduces the use of mosaic tiling to extend the imaged volume for mapping the three-dimensional cytoarchitecture of the entire mouse brain. The author also discusses the challenges in processing these large-scale datasets.