A 3D foundation model unifying CT interpretation and segmentation

Yulu Xie, Zilong Li, Shen Xu, Yifan Bai, Liuhong Shi +12

Radiologists interpret computed tomography (CT) scans by jointly determining what a finding represents and where it lies in three-dimensional (3D) anatomy. However, CT models have treated CT interpretation and 3D segmentation as separate tasks, leaving textual findings spatially unverifiable and overlooking potential synergy between clinical understanding and spatial perception. Here we present HoloCT, a generalist 3D foundation model unifying CT interpretation and voxel-level segmentation by jointly modelling whole-volume context and fine-grained anatomical detail, providing 3D masks as evidence. We curated HoloDATA, comprising 195,921 CT scans from 73 public datasets and six clinical cohorts, with 6.2 million instruction dialogues and 2.8 million CT-mask pairs. Across 346 tasks spanning segmentation, lesion screening, visual question answering, and report generation on 61 internal and 12 external datasets, HoloCT outperformed specialist and foundation models. In multicentre validation across 11,455 clinical CT scans from five hospitals, HoloCT outperformed competing models in lesion segmentation and report generation by 18.2 and 15.3 points. It also achieved 85.1% mean accuracy…