Opportunistic Promptable Segmentation: Leveraging Routine Radiological Annotations to Guide 3D CT Lesion Segmentation.
Authors
Affiliations (3)
Affiliations (3)
- Department of Computer Sciences, University of WI-Madison, Madison, WI, USA. [email protected].
- Department of Radiology, University of WI-Madison, Madison, WI, USA.
- Department of Computer Sciences, University of WI-Madison, Madison, WI, USA.
Abstract
The development of machine learning models for CT imaging depends on the availability of large, high-quality, and diverse annotated datasets. Although large volumes of CT images and reports are readily available in clinical picture archiving and communication systems (PACS), 3D segmentations of critical findings are costly to obtain, typically requiring extensive manual annotation by radiologists. On the other hand, it is common for radiologists to provide limited annotations of findings during routine reads, such as line measurements and arrows, that are often stored in PACS as grayscale softcopy presentation state (GSPS) DICOM objects. We posit that these sparse annotations can be extracted along with CT volumes and converted into 3D segmentations using promptable segmentation models, a paradigm we term Opportunistic Promptable Segmentation. To enable this paradigm, we propose SAM2CT, the first promptable segmentation model designed to convert radiologist annotations, including arrows and lines, into 3D segmentations in CT volumes. SAM2CT extends SAM2 in two ways: the prompt encoder is augmented to accept arrow and line inputs, and a memory-conditioned memory (MCM) module replaces the standard memory encoder's unconditioned features with lesion-conditioned image embeddings, improving propagation accuracy across distant slices in volumetric segmentation. On public lesion segmentation benchmarks, SAM2CT outperforms existing promptable segmentation models and similarly trained baselines, achieving Dice similarity coefficients of 0.649 for arrow prompts and 0.757 for line prompts. Applying the model to pre-existing GSPS annotations from a clinical PACS (N = 60), SAM2CT generates 3D segmentations that are clinically acceptable or require only minor adjustments in 87% of cases, as scored by radiologists. Additionally, SAM2CT demonstrates strong zero-shot performance on select Emergency Department findings (N = 130), including abscesses (DSC = 0.610) and gallstones (DSC = 0.725). These results suggest that large-scale mining of historical GSPS annotations represents a promising and scalable approach for generating 3D CT segmentation datasets.