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![[Figure 2]](gui5004fig2mag.jpg)
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Figure 2
The masking and phase retrieval process, using a rabbit brain cross-section for demonstration. Images are labelled alphabetically according to the order in which they are computed while arrows indicate precursor images required to calculate the subsequent image. (a) A phase-contrast CT slice without any reprocessing applied, beyond flat and dark correction. (b) The same slice phase retrieved for the bone/brain tissue interface [equation (3) ![[link]](../../../../../../logos/arrows/s_arr.gif){kind=small} ], either achieved from 3D phase retrieval of (a) or CT reconstruction of phase retrieved projections. Upon thresholding (b), we create a pixel-wise binary mask of the high-Z material, applying a dilation filter to ensure full enclosure of the high contrast boundaries. The binary mask, (c), is then used to mask all high-Z features out of the raw phase-contrast volume by replacing them with the theoretical low-Z μ value. This creates the image in (d), which is then filtered using 3D phase retrieval of the low-Z material [equation (2)] to make (e). Finally, the high-Z components from the two-material phase retrieved slice (b) are spliced into (e) using the binary mask, resulting in the final phase retrieved image (f), free of over-blurring artefacts from the high-Z boundaries. All non-binary images are displayed on the same colour palette which is optimized for viewing soft tissue features, leading to the bone in (f) appearing over-saturated and the subarachnoid space between the skull and brain tissue seeming indistinguishable from the surrounding agarose the object was set in. |
![[Figure 2]](gui5004fig2.jpg)
 | JOURNAL OF SYNCHROTRON RADIATION |
ISSN: 1600-5775
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