Madrepora oculata sample GeoB12747-1 originates from Meknes mud vulcano, Gulf of Cadiz, where it was taken with the Marum ROV CHEROKEE during Pelagia cruise 64PE284 (position: 34,9883°N, 7.072°W, 714 water depth). The coral colony fragment was scanned by a Toshiba Aquilion 64 computer tomograph (CT) at the hospital Klinikum Bremen-Mitte with an x-ray source voltage of 120 kV and a current of 600 mA. The CT image stack has a resolution of 0.35 mm in x-direction and y-direction and 0.5 mm resolution in z-direction (0.3 mm reconstruction unit). Images were reconstructed using Toshiba's patented helical cone beam reconstruction technique (TCOT) and are provided in DICOM-format.This dataset contains the CT raw data (GeoB12747-1_RawData), the polyp-cavity instance segmentation (GeoB12747-1_cavities) and calices segemntation (GeoB12747-1_calices; given as unique label values) of the polyp-cavity instance segmentation.