Phase-contrast micro-tomography using synchrotron radiation has yielded superior soft tissue visualization down to the
sub-cellular level. The isotropic spatial resolution down to about one micron is comparable to the one of histology. The
methods, however, provide different physical quantities and are thus complementary, also allowing for the extension of
histology into the third dimension. To prepare for cross-sectional animal studies on epilepsy, we have standardized the
specimen’s preparation and scanning procedure for mouse brains, so that subsequent histology remains entirely
unaffected and scanning of all samples (n = 28) is possible in a realistic time frame. For that, we have scanned five
healthy and epileptic mouse brains at the ID19 beamline, ESRF, Grenoble, France, using grating- and propagation-based
phase contrast micro-tomography. The resulting datasets clearly show the cortex, ventricular system, thalamus,
hypothalamus, and hippocampus. Our focus is on the latter, having planned kainate-induced epilepsy experiments. The
cell density and organization in the dentate gyrus and Ammon’s horn region were clearly visualized in control animals.
This proof of principle was required to initiate experiment. The resulting three-dimensional data have been correlated to
histology. The goal is a brain-wide quantification of cell death or structural reorganization associated with epilepsy as
opposed to histology alone that represents small volumes of the total brain only. Thus, the proposed technique bears the
potential to correlate the gold standard in analysis with independently obtained data sets. Such an achievement also fuels
interest for other groups in neuroscience research to closely collaborate with experts in phase micro-tomography.