Images of increment cores acquired with the Gigapixel Woodbot. Software for building your own Gigapixel Woodbot can be found on https://doi.org/10.5281/zenodo.14637832. Releases of software for analysis of the images can be found on https://doi.org/10.5281/zenodo.14637855. The training datasets and trained YOLOv8 model needed to run the analysis, can be found on https://doi.org/10.5281/zenodo.14604996. The full images of the disks (see paper for more details) can be found on https://doi.org/10.6019/S-BIAD1574. This is part of an entire sample preparation, imaging and analysis pipeline available in the paper "Enabling high-throughput quantitative wood anatomy through a dedicated pipeline" by Van den Bulcke and co-authors: https://doi.org/10.1186/s13007-025-01330-7. Cite our paper when using these data.