A modified synchrotron X-ray phase-contrast micro-CT workflow for non-destructive 3D imaging of intestinal biopsies

Visualizing three-dimensional (3D) microstructures of complex biological tissues is crucial for understanding disease progression and environmental stress responses. Here, we report a modified workflow of synchrotron micro-computed tomography (SR-μCT) phase-contrast imaging (PCI) for 3D histology of colon biopsies from ulcerative colitis patients in remission (UCr), by refining the sample preparation method and data processing for improved image quality and processing of large synchrotron datasets. Our studies showed that samples prepared by critical-point-dried (CPD) markedly enhanced intrinsic contrast relative to paraffin-embedded specimens, enabling delineation of tissue microarchitecture and the reliability of digital segmentation. Additionally, we developed a scalable data orchestration workflow (Tiffy McSliceface, TMSF) that enabled segmentation of full-resolution volumetric datasets through structured sparse annotation and smart interpolation. This approach eliminates the need for binning, cropping, or bit-depth reduction, thereby improving processing speed and overall efficiency. As a proof-of-concept, we employed the proposed workflow for SR-μCT-PCI to visualize and quantify microstructural alterations in biopsies exposed to the food additive titanium dioxide (E171) ex vivo, revealing disrupted 3D crypt lumen interconnectivity. In short, our studies showed the possibility of simplifying large synchrotron data processing and supports high-throughput 3D analysis for investigating gastrointestinal pathology and tissue responses to environmental stressors.