A knowledge-integrated deep learning framework for cellular image analysis in parasite microbiology

Cellular image analysis is an important method for microbiologists to identify and study microbes. Here, we present a knowledge-integrated deep learning framework for cellular image analysis, using three tasks as examples: classification, detection, and reconstruction. Alongside thorough descriptions of different models and datasets, we describe steps for computing environment setup, knowledge representation, data pre-processing, and training and tuning. We then detail evaluation and visualization. For complete details on the use and execution of this protocol, please refer to Li et al. (2021),¹ Jiang et al. (2020),² and Zhang et al. (2022).³.