Feature-prompting GBMSeg: One-Shot Reference Guided Training-Free Prompt Engineering for Glomerular Basement Membrane Segmentation

Assessment of the glomerular basement membrane (GBM) in transmission electron microscopy (TEM) is crucial for diagnosing chronic kidney disease (CKD). The lack of domain-independent automatic segmentation tools for the GBM necessitates an AI-based solution to automate the process. In this study, we introduce GBMSeg, a training-free framework designed to automatically segment the GBM in TEM images guided only by a one-shot annotated reference. Specifically, GBMSeg first exploits the robust feature matching capabilities of the pretrained foundation model to generate initial prompt points, then introduces a series of novel automatic prompt engineering techniques across the feature and physical space to optimize the prompt scheme. Finally, GBMSeg employs a class-agnostic foundation segmentation model with the generated prompt scheme to obtain accurate segmentation results. Experimental results on our collected 2538 TEM images confirm that GBMSeg achieves superior segmentation performance with a Dice similarity coefficient (DSC) of 87.27% using only one labeled reference image in a training-free manner, outperforming recently proposed one-shot or few-shot methods. In summary, GBMSeg introduces a distinctive automatic prompt framework that facilitates robust domain-independent segmentation performance without training, particularly advancing the automatic prompting of foundation segmentation models for medical images. Future work involves automating the thickness measurement of segmented GBM and quantifying pathological indicators, holding significant potential for advancing pathology assessments in clinical applications. The source code is available on https://github.com/SnowRain510/GBMSeg

MSA-MIL: A deep residual multiple instance learning model based on multi-scale annotation for classification and visualization of glomerular spikes

Membranous nephropathy (MN) is a frequent type of adult nephrotic syndrome, which has a high clinical incidence and can cause various complications. In the biopsy microscope slide of membranous nephropathy, spikelike projections on the glomerular basement membrane is a prominent feature of the MN. However, due to the whole biopsy slide contains large number of glomeruli, and each glomerulus includes many spike lesions, the pathological feature of the spikes is not obvious. It thus is time-consuming for doctors to diagnose glomerulus one by one and is difficult for pathologists with less experience to diagnose. In this paper, we establish a visualized classification model based on the multi-scale annotation multi-instance learning (MSA-MIL) to achieve glomerular classification and spikes visualization. The MSA-MIL model mainly involves three parts. Firstly, U-Net is used to extract the region of the glomeruli to ensure that the features learned by the succeeding algorithm are focused inside the glomeruli itself. Secondly, we use MIL to train an instance-level classifier combined with MSA method to enhance the learning ability of the network by adding a location-level labeled reinforced dataset, thereby obtaining an example-level feature representation with rich semantics. Lastly, the predicted scores of each tile in the image are summarized to obtain glomerular classification and visualization of the classification results of the spikes via the usage of sliding window method. The experimental results confirm that the proposed MSA-MIL model can effectively and accurately classify normal glomeruli and spiked glomerulus and visualize the position of spikes in the glomerulus. Therefore, the proposed model can provide a good foundation for assisting the clinical doctors to diagnose the glomerular membranous nephropathy.