Kidney abnormality segmentation in thorax-abdomen CT scans
Gabriel Efrain Humpire Mamani Nikolas Lessmann Ernst Th. Scholten Mathias Prokop Colin Jacobs Bram van Ginneken
In this study, we introduce a deep learning approach for segmenting kidney
parenchyma and kidney abnormalities to support clinicians in identifying and
quantifying renal abnormalities such as cysts, lesions, masses, metastases, and
primary tumors. Our end-to-end segmentation method was trained on 215
contrast-enhanced thoracic-abdominal CT scans, with half of these scans
containing one or more abnormalities.
  We began by implementing our own version of the original 3D U-Net network and
incorporated four additional components: an end-to-end multi-resolution
approach, a set of task-specific data augmentations, a modified loss function
using top-$k$, and spatial dropout. Furthermore, we devised a tailored
post-processing strategy. Ablation studies demonstrated that each of the four
modifications enhanced kidney abnormality segmentation performance, while three
out of four improved kidney parenchyma segmentation. Subsequently, we trained
the nnUNet framework on our dataset. By ensembling the optimized 3D U-Net and
the nnUNet with our specialized post-processing, we achieved marginally
superior results.
  Our best-performing model attained Dice scores of 0.965 and 0.947 for
segmenting kidney parenchyma in two test sets (20 scans without abnormalities
and 30 with abnormalities), outperforming an independent human observer who
scored 0.944 and 0.925, respectively. In segmenting kidney abnormalities within
the 30 test scans containing them, the top-performing method achieved a Dice
score of 0.585, while an independent second human observer reached a score of
0.664, suggesting potential for further improvement in computerized methods.
  All training data is available to the research community under a CC-BY 4.0
license on https://doi.org/10.5281/zenodo.8014289