Volume electron microscopy (EM) techniques, such as focused ion beam scanning electron microscopy (FIB-SEM) enable 3D imaging of cells and subcellular structures at very high resolution. However, these methods involve sectioning of the specimen, thereby destroying the sample for further study. Ptychographic X-ray computer cryo-tomography (PXCT) is a novel, non-destructive imaging method that can image large volumes due to the excellent penetration of hard X-rays into the sample. In this Tools and Resources paper, Valerie Panneels and colleagues (Panneels et al., 2021) implement PXCT to study the 3D organisation of the retina. Using this technique, the authors perform a non-destructive scan of a retina sample containing ∼60 photoreceptor cell bodies. Here, the isotropic resolution of 150–200 nm allows the visualisation of subcellular structures, such as mitochondria and synaptic ribbons. Moreover, PXCT reveals pronounced degeneration of photoreceptors in the retina of mice models of retinitis pigmentosa compared to those of wild-type mice. Taking advantage of the preservative nature of the approach, the authors perform correlative imaging using FIB-SEM to assess the complementarity of the two techniques and show that subcellular features observed in PXCT match the EM data. Overall, PXCT is a powerful non-destructive method for imaging large tissue volumes at sub-200 nm resolution that allows for further investigations, such as correlative imaging, proteomics and genomic analysis.