Semantic Instance Segmentation of Kidney Cysts in MR Images: A Fully Automated 3D Approach Developed Through Active Learning

Adriana V. Gregory, Deema A. Anaam, Andrew J. Vercnocke, Marie E. Edwards, Vicente E. Torres, Peter C. Harris, Bradley J. Erickson, Timothy L. Kline

Research output: Contribution to journalArticlepeer-review


Total kidney volume (TKV) is the main imaging biomarker used to monitor disease progression and to classify patients affected by autosomal dominant polycystic kidney disease (ADPKD) for clinical trials. However, patients with similar TKVs may have drastically different cystic presentations and phenotypes. In an effort to quantify these cystic differences, we developed the first 3D semantic instance cyst segmentation algorithm for kidneys in MR images. We have reformulated both the object detection/localization task and the instance-based segmentation task into a semantic segmentation task. This allowed us to solve this unique imaging problem efficiently, even for patients with thousands of cysts. To do this, a convolutional neural network (CNN) was trained to learn cyst edges and cyst cores. Images were converted from instance cyst segmentations to semantic edge-core segmentations by applying a 3D erosion morphology operator to up-sampled versions of the images. The reduced cysts were labeled as core; the eroded areas were dilated in 2D and labeled as edge. The network was trained on 30 MR images and validated on 10 MR images using a fourfold cross-validation procedure. The final ensemble model was tested on 20 MR images not seen during the initial training/validation. The results from the test set were compared to segmentations from two readers. The presented model achieved an averaged R2 value of 0.94 for cyst count, 1.00 for total cyst volume, 0.94 for cystic index, and an averaged Dice coefficient of 0.85. These results demonstrate the feasibility of performing cyst segmentations automatically in ADPKD patients.

Original languageEnglish (US)
Pages (from-to)773-787
Number of pages15
JournalJournal of Digital Imaging
Issue number4
StatePublished - Aug 2021


  • Autosomal dominant polycystic kidney disease
  • Convolutional neural networks
  • Cyst volume
  • Magnetic resonance imaging
  • Three-dimensional instance segmentation

ASJC Scopus subject areas

  • Radiological and Ultrasound Technology
  • Radiology Nuclear Medicine and imaging
  • Computer Science Applications


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