Phase-contrast micro computed tomography for vasculature imaging in post mortem human brain stem

Studying the vasculature in the human brain using classical histology can be challenging due to the necessity for high quality, stained tissue slices. Here, we propose to use phase-contrast micro computed tomography (microCT) for identifying the vasculature in the unstained, paraffin-embedded brain. With a phase contrast technique, which incorporates the phase shift of the X-rays, we could obtain edge enhanced images from the tectum of the midbrain. Human brain stems were provided by the University of Tübingen Body Donor program. Samples were fixed in formaldehyde for a minimum of 4 weeks and then were embedded in paraffin. Acquisitions were made at the SYRMEP beamline of the Elettra Synchrotron Facility in the “white-beam” configuration mode, illuminating the sample with a mean energy of 22 keV. The samples were measured with a rotation angle of 180° with a total of 3600 projections. We scanned 4 samples in 4.9μm pixel size (detector-to-sample-distance, DSD: 90cm) and 2 samples in 0.9μm pixel size (DSD: 20cm). We applied Paganin’s phase retrieval algorithm for signal-to-noise ratio improvement and filtered back projection for image reconstruction. Vessels were automatically segmented using; a median filter, non-local means denoising, a variance filter followed by thresholding and opening. Vessel volume within the superior colliculus was calculated using 0.9μm pixel size data. Figure 1 shows that the vessel structure segmented from microCT matches the structure revealed by Indian ink staining in a previous study (Durvernoy, H. M., 1978.). Within the superior colliculus, vessels project from the surface towards the cerebral aqueduct in a parallel manner. Within the superior colliculi, vessel volume made up a mean of 3.47 % (SD= 0.53%) of the tissue. These findings show that phase contrast microCT is suitable for investigating the vasculature of post mortem human brain. This method can also be used for vessel tracing in three dimensional space and analyzing features such as length, diameter and branching