Multi-planar 2D-U-Net Segmentation of 3D-CT Abdominal Organs augmented by Spatial Occurrence Maps
Authors: Daria Kern, Negar Chabi, Souraj Adhikary, Andre Mastmeyer
Abstract
This work proposes a lightweight 2D-U-Net-based framework for segmenting five abdominal organs in large field-of-view 3D CT scans. The method combines coarse-to-fine segmentation, predictions from multiple anatomical planes, and additional fuzzy 3D spatial maps that provide anatomical location cues to improve segmentation accuracy. We combine multi-planar 2D-U-Net models augmented by a spatial occurrence map. The approach involves two main stages. First, the abdominal volume of interest region is detected by traversing the whole scan axially with a 2D-U-Net and determining the x-y-z-minimum and -maximum extents of the 5 abdominal organs of interest. Second, we use spatial occurrence maps to enhance our multi-planar 2D-U-net architecture inside the bounds from the former stage. The method is evaluated on 80 CT scans from various public sources. The results show Dice improvements of about 4% at maximum compared to the same model trained without spatial occurrence maps.
Reliable organ localization in abdominal CT can provide spatial priors for downstream trauma analysis. We propose CT-3GDINO, a lightweight 3D detector that adapts a Grounding-DINO-style query-based architecture to fixed organ localization using frozen pseudo-text class tokens instead of a real text encoder. The model combines a Swin3D visual backbone, bidirectional feature enhancement, pseudo-text-guided query selection, and a cross-modality decoder to predict normalized 3D boxes for liver, spleen, left kidney, right kidney, and bowel. We train and evaluate on 193 matched RSNA/RATIC CT volumes with segmentation-derived boxes. The best multi-scale model, trained from scratch, achieves 0.5830 overall top-1 class-wise mAP over 3D IoU thresholds from 0.1 to 0.7, outperforming fixed- and trainable-backbone classification-pretrained variants with 0.5570 and 0.4657 mAP. Performance is strong for coarse localization, with 0.9649 AP at IoU 0.1, but remains limited for strict box alignment, with 0.1552 AP at IoU 0.7. These results establish CT-3GDINO as an open-source baseline for pseudo-text-conditioned 3D organ localization and motivate future work on localization-aware pretraining, richer multimodal conditioning, and injury-focused detection.
In this retrospective multi-institutional study, a quantitative phenotyping framework, CT-IDP (CT Image-Derived Phenotypes) was developed on the MERLIN abdominal CT benchmark (training, validation, and test sets- 15,175, 5,018, and 5,082 studies, respectively) and externally evaluated on two independent dataset: Duke-Abdomen (2,000) and AMOS (1,107). Multi-organ segmentations were generated with TotalSegmentator and used to derive over 900 organ and compartment-level descriptors spanning morphometry, attenuation, and contextual/burden findings. Sparse disease-specific logistic regression with elastic-net regularization was trained on MERLIN and externally validated under a frozen specification. Performance was compared against a DINOv3-based vision-transformer baseline using AUC and average precision (AP), supported by phenotype-stratified audits and coefficient-level inspection. Macro-AUC for CT-IDP versus the baseline was 0.897 versus 0.880 on MERLIN, 0.877 versus 0.857 on the Duke-Abdomen dataset, and 0.780 versus 0.756 on AMOS.
Abdominal CT disease classification is challenging because each scan is a large 3D volume with many possible findings, while diagnostic evidence is often confined to specific organs or anatomical compartments. Most study-level classifiers aggregate encoder features using anatomy-agnostic pooling or attention, creating a mismatch between localized disease evidence and global evidence aggregation. We propose ORACLE--CT, an encoder-agnostic anatomy-aware aggregation framework that uses multi-organ segmentation to define label-specific anatomical supports and restrict attention pooling to relevant regions. The framework supports single-organ, multi-organ union, comparative, localized, and global support strategies. We evaluate ORACLE--CT with three encoder families: DINOv3, I3D--ResNet-121, and the radiology-native Pillar--0 encoder. Models are trained end-to-end on MERLIN and evaluated internally and under frozen external transfer to Duke--Abdomen and AMOS. Compared with global average pooling, support-masked pooling improved MERLIN macro-AUROC/AUPRC from 0.838/0.638 to 0.858/0.676 for DINOv3 and from 0.829/0.617 to 0.848/0.659 for I3D--ResNet-121. On harmonized 10-label external evaluation, DINOv3 improved on Duke--Abdomen from 0.802/0.628 to 0.835/0.683 and on AMOS from 0.742/0.313 to 0.762/0.350, with similar gains for I3D--ResNet-121. For Pillar--0, most gains came from learned attention, with smaller additional benefit from anatomical masking. ORACLE--CT improves discrimination and external robustness while preserving an auditable link between predictions and anatomical evidence.