Transport of immune cells, nutrients and waste products via the cerebrospinal fluid (CSF) has been implicated in the development of neurological disorders. Using time-resolved in vivo microtomography, we investigated pulsatile motion of CSF spaces in the mouse brain as a potential driver of CSF flow. Here we present a method for detecting motion captured in murine brain images acquired in vivo at the European Synchrotron Radiation Facility. Anesthetized mice were placed in a heated holder that was designed to minimize head motion and maintain physiological body temperature. Contrast agent was infused into the ventricle to improve visibility of the CSF spaces. Projections were retrospectively sorted based on the ECG recording. Cardiac phase images were reconstructed in 10ms intervals from the ECG peak and automatically analyzed for decorrelation. Motion was automatically quantified by non-rigid registration. Regions with high intensity structures, large motion magnitudes, large improvements in image similarity due to registration, or at the contrast-enhanced ventricles were visually inspected for structures with motion artifacts prior to registration. We detected mainly motion in the nasopharynx, skin, ear channels, and bones in the range of 2.3 to 14.8µm magnitude. Small motion artifacts were detectable only for high-contrast structures. No misalignments were visible for the contrast-enhanced ventricles at a voxel resolution of 6.30 to 6.45µm. In the future, dedicated active gating to ensure regular sampling and local scans with improved spatial resolution will be used to investigate the limits to the detection of in vivo ventricular motion in mice.
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.
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