3D visualization and detection of glomeruli in whole mouse kidney

The kidney is an important organ in the body to excrete metabolic waste, and the glomerulus is an essential structure for the kidney to play a role in blood filtration. Abnormal glomerular numbers are associated with nephropathy or circulatory disease. With the development of imaging technology, mesoscopic optical imaging can obtain whole kidney images at single cell resolution. The detection of glomeruli from images is very crucial for understanding the renal function and studying nephropathy. Existing detection methods cannot balance both accuracy and efficiency, so we proposed a deep learning-based glomeruli detection method. First, we imaged an entire mouse kidney with High-Definition fluorescent Micro-Optical Sectioning Tomography (HD-fMOST) and obtained a three-dimensional (3D) kidney image at cellular resolution. Then, we designed an end-to-end 3D convolutional neural network based on the morphological features of glomeruli in the kidney image, which can directly read 3D images and predict the precise coordinates of glomeruli. We used the acquired kidney dataset to train the network and validated the effect of glomeruli detection. Finally, we applied our approach to detect glomeruli in large-scale mouse kidney. The results showed that the proposed method reached the state-of-the-art level, which is more efficient and accurate compared to similar methods. The proposed method will provide a powerful tool for kidney-related research.