Lophelia pertusa colony sample SaM-ID43148 was retrieved during Meteor cruise M70-1 with the ROV MARUM-Quest from the Gondola Slide, southeast of the Gargano Promontory in the Adriatic Sea. The specimen was scanned with a Philips Brilliance iCT Elite 256 computer tomograph (x-ray source, voltage: 120 kV; current: 300 mA; physical resolution: 0.313 in xy-direction, respectively, 0.625 mm in z-direction; re-construction interval in z-direction: 0.3 mm; reconstruction: filtered Back Projection (fBP) mode and a bone kernel (YB (Enhanced)). The orginal scan including the polyp-cavity instance segmentation is provided here: https://doi.org/10.1594/PANGAEA.947300). This dataset contains the calices segmentation (given as unique label values) for the polyp-cavity instance segmentation and a spreadsheet containing the (directed) edges of the colony skeleton graph. Each label in SaM-ID43148_calices represents a vertex in this graph. The edges are given by their start label Node ID #1 and the label of their target Node ID #2.