Quantitative 3D imaging of organelle remodeling in disease models with soft X-ray tomography

Jian-Hua Chen^1,2*

¹X-Ray Imaging Group, Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
²Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

* Presenter:Jian-Hua Chen, email:chen.jh@nsrrc.org.tw

High-throughput 3D volumetric imaging has gained significant attention in recent years owing to rapid advances in imaging technologies and computational power. Among these, soft X-ray tomography (SXT) has emerged as an innovative, label-free imaging platform for visualizing intact, cryo-preserved cells in 3D with nanoscale resolution. Operating within the “water-window” (284–543 eV), SXT maps the linear absorption coefficients (LACs) of subcellular components, enabling direct structural analysis without complex labeling or physical sectioning[1] . A key advantage of SXT is the isotropic reconstruction enabled by full-rotation capillary sample holders. This geometry allows for continuous 360° data acquisition, eliminating missing-wedge artifacts inherent to grid-based setups. The isotropic reconstruction results in uniform spatial resolution across all directions and enables accurate volumetric quantification of organelle morphology and spatial organization[2] .
SXT has been applied to a variety of disease models. In cancer research, it enables detailed 3D visualization of nuclear architecture, revealing alterations in nuclear size, shape, and chromatin organization[3] . During viral infections, such as those caused by herpes simplex virus (HSV-1) and SARS-CoV-2, SXT captures dynamic remodeling of host cells, including the formation of replication centers and multivesicular bodies[4,5] . Moreover, SXT is particularly effective for visualizing membraneless organelles formed through liquid–liquid phase separation (LLPS) without perturbing the native cellular state[6] . Together, these results demonstrate that SXT serves as a high-throughput, quantitative imaging platform for visualizing and measuring subcellular structural changes associated with disease.

[1] Ekman A A, Chen J, Guo J, McDermott G, Gros M A L and Larabell C A 2017 Mesoscale imaging with cryo‐light and X‐rays: Larger than molecular machines, smaller than a cell Biol Cell 109 24–38
[2] Weinhardt V and Larabell C 2025 Soft X-Ray Tomography Has Evolved into a Powerful Tool for Revealing Cell Structures. Annu. Rev. Anal. Chem. 18 427–46
[3] Chen J-H, Ekman A, Weinhardt V, Loconte V, Dermott G M, Gros M A L and Larabell C 2020 Imaging Sub-cellular 3D Structures Using Soft X-ray Microscopy Microscopy and Microanalysis 26 2782–3
[4] Loconte V, Chen J-H, Cortese M, Ekman A, Gros M A L, Larabell C, Bartenschlager R and Weinhardt V 2021 Using soft X-ray tomography for rapid whole-cell quantitative imaging of SARS-CoV-2-infected cells Cell Reports Methods 100117
[5] Chen J-H, Vanslembrouck B, Ekman A, Aho V, Larabell C A, Gros M A L, Vihinen-Ranta M and Weinhardt V 2022 Soft X-ray Tomography Reveals HSV-1-Induced Remodeling of Human B Cells Viruses 14 2651
[6] Sansevrino R, Hoffmann C, Chen J-H, Tromm J V, Jackson J, Gros M L, Bano D, Larabell C and Milovanovic D 2023 Lewy Body-Like Condensates Sequester Membrane-Bound Organelles Microscopy and Microanalysis 29 1157–1157

Keywords: Soft X-ray tomography, 3D isotropic quantitative imaging , Linear absorption coefficient (LAC)