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
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