An imaging framework for nuclei-based three-dimensional cell quantification in intact tissue using phase-contrast X-ray CT

Objective. Quantitative analysis of cellular morphology and spatial organisation within intact tissue remains challenging, particularly when three-dimensional information must be preserved. This study investigates whether laboratory propagation-based phase-contrast X-ray computed tomography (CT) can support nuclei-based quantitative analysis in unstained tissue while retaining the surrounding tissue architecture. Approach. We propose a nuclei-based quantitative imaging workflow that combines laboratory propagation-based phase-contrast X-ray CT with volumetric segmentation. Intact unstained liver tissue was imaged at cellular resolution, then nuclei were segmented throughout the reconstructed volume and quantitative metrics describing the nuclear morphology and spatial organisation were extracted. The resulting measurements were evaluated in two non-overlapping volumes of interest and compared with histological reference data using thickness-matched virtual CT slices. Main results. The proposed workflow enabled visualisation and segmentation of individual nuclei throughout intact unstained liver tissue. Comparable nuclear morphology and spatial organisation metrics were obtained from two non-overlapping volumes of interest, indicating stable segmentation performance within the analysed specimen. Comparison with H&E histology demonstrated broad agreement in nuclear morphology. Significance. This work demonstrates the feasibility of nuclei-based quantitative analysis using laboratory phase-contrast X-ray CT in intact unstained tissue. The approach provides volumetric cellular information while preserving tissue architecture and may complement conventional histological assessment in applications requiring three- dimensional analysis. These findings highlight the potential of laboratory phase-contrast CT for quantitative tissue characterisation and spatial cellular analysis