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Accurate microscopic images segmentation of activated sludge is essential for monitoring wastewater treatment processes. However, it is a challenging task due to poor contrast, artifacts, morphological similarities, and distribution imbalance. A novel image segmentation model (FafFormer) was developed in the work based on Transformer that incorporated pyramid pooling and flow alignment fusion. Pyramid Pooling Module was used to extract multi-scale features of flocs and filamentous bacteria with different morphology in the encoder. Multi-scale features were fused by flow alignment fusion module in the decoder. The module used generated semantic flow as auxiliary information to restore boundary details and facilitate fine-grained upsampling. The Focal–Lovász Loss was designed to handle class imbalance for filamentous bacteria and flocs. Image-segmentation experiments were conducted on an activated …