Practical Guidelines for Cell Segmentation Models Under Optical Aberrations in Microscopy
This work addresses a critical challenge in biomedical research by providing practical guidelines for cell segmentation under optical aberrations, though it is incremental as it builds on existing models and datasets.
This study tackled the problem of cell segmentation models being unreliable under microscope optical aberrations by evaluating various models on simulated aberrations, finding that FPN with SwinS backbone is robust for simple images and Cellpose 2.0 for complex ones, and proposing a PLCM model to identify aberration types with high accuracy (e.g., 95% on test sets).
Cell segmentation is essential in biomedical research for analyzing cellular morphology and behavior. Deep learning methods, particularly convolutional neural networks (CNNs), have revolutionized cell segmentation by extracting intricate features from images. However, the robustness of these methods under microscope optical aberrations remains a critical challenge. This study evaluates cell image segmentation models under optical aberrations from fluorescence and bright field microscopy. By simulating different types of aberrations, including astigmatism, coma, spherical aberration, trefoil, and mixed aberrations, we conduct a thorough evaluation of various cell instance segmentation models using the DynamicNuclearNet (DNN) and LIVECell datasets, representing fluorescence and bright field microscopy cell datasets, respectively. We train and test several segmentation models, including the Otsu threshold method and Mask R-CNN with different network heads (FPN, C3) and backbones (ResNet, VGG, Swin Transformer), under aberrated conditions. Additionally, we provide usage recommendations for the Cellpose 2.0 Toolbox on complex cell degradation images. The results indicate that the combination of FPN and SwinS demonstrates superior robustness in handling simple cell images affected by minor aberrations. In contrast, Cellpose 2.0 proves effective for complex cell images under similar conditions. Furthermore, we innovatively propose the Point Spread Function Image Label Classification Model (PLCM). This model can quickly and accurately identify aberration types and amplitudes from PSF images, assisting researchers without optical training. Through PLCM, researchers can better apply our proposed cell segmentation guidelines.