Intravital microscopy (IVM) imaging has afforded important insights into tumour metastasis, but its resolution is insufficient to reveal events at the subcellular level or the interactions between tumour cells and the surrounding tissue. Correlation of IVM with 3D electron microscopy (EM) has a great potential, but the retrieval of single objects after EM is difficult. In this ‘Tools and Techniques’ article (p. 444), Jacky G. Goetz, Yannick Schwab and co-workers present a new approach that exploits microscopic X-ray computed tomography (microCT) to precisely correlate IVM images with the EM-processed sample. To demonstrate the power of their methodology, the authors intracardially xenografted single tumour cells into a living mouse to model metastasis to the brain. After IVM imaging, the region of interest (ROI) is marked near the brain cortex surface using near-infrared branding; this allows precise dissection of a sample containing the ROI volume, which is then processed for EM and embedded in resin. Scanning the tissue with microCT highlights anatomical landmarks that enable the prediction of the position of the cell within the sample block. Using this workflow, the authors could observe tumour cell extensions and remodelling of the endothelial layer close to the tumour cell, providing unprecedented insights into early steps of extravasation in vivo. Because this approach is highly versatile, it can be applied to other cellular events that can be imaged in vivo and, thus, might become a routine approach to understand biological processes at the subcellular level.