GUI Based Fuzzy Logic and Spatial Statistics for Unsupervised Microscopy Segmentation

Abstract: Brightfield microscopy imaging of unstained live cells remains a persistent challenge due to low contrast, temporal changes in specimen phenotypes, irregular illumination, and the absence of training labels. While deep learning (DL) methods (e.g., Cellpose 3.0) achieve state-of-the-art (SOTA) performance, they require extensive labeled data and heavy computational resources, and they often fail under uneven illumination. We present the first unsupervised segmentation framework combining spatial standard deviation from local mean (SSDLM), fuzzy logic, adjusted variograms, Moran's I, and cumulative squared shift of nodal intensity (CSSNI) to address these limitations. Unlike deep learning models, our approach requires no annotations or retraining and operates through a user-friendly GUI tailored for non-programming users. The robustness and generality were validated on three datasets, including cross-domain data. We benchmark our method against 2023--2024 SOTA models, including Cellpose 3.0 and StarDist, using a dataset of unstained myoblast images. Our method achieves a significant improvement in segmentation performance, with an IoU increase of up to 48\% and statistically validated superiority ($p < 0.01$, Wilcoxon signed-rank test). Expert evaluation from two biologists further supports the segmentation quality (Cohen's $\kappa > 0.75$). The proposed algorithm is lightweight, interpretable, and computationally efficient, offering a practical and effective alternative for cell segmentation in label-free microscopy. The code, the dataset, and the results are available for reproducibility*.