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

Griffin Rodgers; Christine Tanner; Georg Schulz; Timm Weitkamp; Mario Scheel; Marta Girona Alarcón; Vartan Kurtcuoglu; Bert Müller

doi:10.1117/12.2633556

14 October 2022 Mosaic microtomography of a full mouse brain with sub-micron pixel size

Griffin Rodgers, Christine Tanner, Georg Schulz, Timm Weitkamp, Mario Scheel, Marta Girona Alarcón, Vartan Kurtcuoglu, Bert Müller

Author Affiliations +

Proceedings Volume 12242, Developments in X-Ray Tomography XIV; 122421L (2022) https://doi.org/10.1117/12.2633556
Event: SPIE Optical Engineering + Applications, 2022, San Diego, California, United States

Abstract

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-µm pixel size, reconstructed volume is limited to about a few mm3 . For full brain mapping, even for the mouse brain with volume of 450 mm3 , the field-of-view must be significantly increased in all three dimensions. We demonstrate mosaic tiling to extend imaged volume by 400× and a dedicated pipeline to process these tera-voxel sized datasets. Here, an entire mouse brain was imaged with 0.65 µm-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.

Citation Download Citation

Griffin Rodgers, Christine Tanner, Georg Schulz, Timm Weitkamp, Mario Scheel, Marta Girona Alarcón, Vartan Kurtcuoglu, and Bert Müller "Mosaic microtomography of a full mouse brain with sub-micron pixel size", Proc. SPIE 12242, Developments in X-Ray Tomography XIV, 122421L (14 October 2022); https://doi.org/10.1117/12.2633556

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