XBRAIN: X-ray Brain Reconstruction, Analytics, and Inference for Neuroscience

Reconstructing neuroanatomical samples in three dimensions (3D) is challenging, as traditional methods require fine sectioning of tissue and alignment of these sections into a 3D volume. In this manuscript, we present a pipeline for quantifying neuroanatomy with synchrotron X-ray microtomography (μCT), a method that achieves micron resolution over thick millimeter-scale intact samples. As brain tissue can be imaged with μCT without damaging the integrity of the sample, electron microscopy was applied to survey higher-resolution structures. We introduce this data analysis pipeline for blood vessel segmentation and cell detection, as well as producing estimates of cell densities and spatial relationships among cells and blood vessels. These methods promise efficient imaging, reconstruction, and analysis of brain structures using μCT.