RDMP: A Reference Detection and Mask Propagation Pipeline for Numerous 3D Glomeruli Segmentation in Large Volumes

Quantitative analysis of numerous repetitive structures in large volumes is one of the most challenging tasks in biomedical imaging, primarily due to its intensive manual requirements. Kidney glomeruli exemplify this challenge due to their dispersion across the cortical region, high density and microscopic size. To address this, we present a Reference Detection and Mask Propagation (RDMP) pipeline that combines object detection with 2D and 3D mask propagation, gradually achieving efficient segmentation of the entire volume by using a 2D reference example. Our method demonstrates robust performance, achieving a Dice Similarity Coefficient (DSC) of 0.9096 on microCT data, and when generalized to Synchrotron Radiation X-ray (SRX) data, reaching a DSC of 0.8431 with only minimal bounding box fine-tuning. Overall, this pipeline shows strong potential for efficient, large-scale kidney analysis, significantly reducing labor demands and accelerating kidney disease research.