Anchored Slice Propagation with Boundary Transport for 3D CT Segmentation from Three Orthogonal Annotated Slices

Dense voxel-level annotation remains a major bottleneck in 3D medical image segmentation. Single-slice propagation methods such as Sli2Vol reduce this burden by propagating one annotated seed slice through a volume using label-free registration. However, axial-only propagation accumulates errors with distance from the seed, especially in surface-distance metrics, because it ignores coronal and sagittal evidence and therefore underuses the 3D information available in CT/MRI volumes. To better leverage volumetric geometry, we study how key training and inference choices affect slice-propagation models, including single-axis versus multi-axis label-free registration, single-seed versus multi-seed propagation, and orthogonal seed configurations. Instead of propagating from a single axial seed, we use three orthogonal seeds---one axial, one coronal, and one sagittal---and fuse their propagated labels with a simple label-free rule. Our results show that the training paradigm has limited impact: an axially trained network applied to off-axis seeds captures nearly all the improvement, while explicit three-axis training adds little. Instead, performance is driven by inference-time seed geometry, especially orthogonality rather than the number of annotated slices, as a budget-matched three-axial control provides no benefit and can even degrade performance. On a multi-organ CT cohort, orthogonal seeding with the axial Sli2Vol backbone improves Dice by 21.9%, Normalized Surface Dice by 25.5%, and reduces Average Hausdorff Distance by 53.5% over the single-axis baseline.

Visual grounding models can enhance radiology workflows by linking report findings to image regions. This is particularly valuable for 3D CT, where findings often occupy a tiny fraction of the volume. Training 3D grounding models requires large sets of paired phrases and regions, and building such datasets is expensive, requiring radiologists to annotate images by hand. We posit that this supervision is already created implicitly during routine reporting, as radiologists frequently place 2D annotations (e.g., distance measurement, arrows) on key images to make measurements and to support report interpretation. We introduce an automated pipeline that converts these routine clinical annotations into large-scale phrase-region supervision for 3D visual grounding. The pipeline links each annotation to the corresponding finding in the report through metadata matching, then uses a promptable 3D segmentation model to convert the 2D annotation into a volumetric mask. This produces phrase-mask-volume datasets without requiring additional radiologist annotation. Applied to a single institution's clinical picture archiving and communication system (PACS), our approach generated 105K phrase-mask-volume triplets from 59K abdominal CT exams. We also introduce two abdominal CT grounding benchmarks, LocusBench-Onc and LocusBench-ED, which comprise 240 oncology and 260 emergency-department radiologist-reviewed phrase-mask-volume triplets, respectively, with the latter spanning 13 distinct categories such as appendicitis, hematoma, and hernia. We further introduce LocusCT, a 3D visual grounding model trained on this dataset, which achieves hit rates of 0.725 on LocusBench-Onc and 0.773 on LocusBench-ED, substantially outperforming comparator models. These results show that routine PACS annotations are a scalable, previously unused source of supervision for 3D visual grounding.

Accurate 3D abnormality segmentation in chest CT requires dense spatial supervision, but obtaining expert voxel-level labels is costly. Radiology reports, however, are routinely generated during clinical interpretation and contain instance-specific descriptions that can provide additional guidance without new dense annotation. Existing vision-language grounding methods typically require report-derived findings at inference, making localization dependent on paired text and limiting each forward pass to a queried finding. We propose Instance-Guided Report Anchoring (IGRA), a model-agnostic module that preserves the correspondence between each annotated abnormality instance and the report finding that describes it. IGRA pools each instance representation and anchors it to the corresponding finding embedding during training; all text-related components are discarded at inference. We further reformulate free-text grounding on ReXGroundingCT as multi-label volumetric segmentation by merging same-category instances, allowing all abnormality categories to be predicted in one image-only forward pass. IGRA improves Dice by 22.5% over the strongest image-only baseline (30.93 vs. 25.25) and is comparable to VoxTell on the single-finding subset (30.29 vs. 30.43). Applied unchanged to four standard 3D segmentation backbones, IGRA improves Dice and hit rate across all architectures. Zero-shot evaluation on LIDC-IDRI, PleThora, and a private in-house dataset further shows consistent gains over image-only baselines.