A reliable and low-cost deep learning model integrating convolutional neural network and transformer structure for fine-grained classification of chicken Eimeria species

Chicken coccidiosis is a disease caused by Eimeria spp. and costs the broiler industry more than 14 billion dollars per year globally. Different chicken Eimeria species vary significantly in pathogenicity and virulence, so the classification of different chicken Eimeria species is of great significance for the epidemiological survey and related prevention and control. The microscopic morphological examination for their classification was widely used in clinical applications, but it is a time-consuming task and needs expertise. To increase the classification efficiency and accuracy, a novel model integrating transformer and convolutional neural network (CNN), named Residual-Transformer-Fine-Grained (ResTFG), was proposed and evaluated for fine-grained classification of microscopic images of seven chicken Eimeria species. The results showed that ResTFG achieved the best performance with high accuracy and low cost compared with traditional models. Specifically, the parameters, inference speed and overall accuracy of ResTFG are 1.95M, 256 FPS and 96.9%, respectively, which are 10.9 times lighter, 1.5 times faster and 2.7% higher in accuracy than the benchmark model. In addition, ResTFG showed better performance on the classification of the more virulent species. The results of ablation experiments showed that CNN or Transformer alone had model accuracies of only 89.8% and 87.0%, which proved that the improved performance of ResTFG was benefit from the complementary effect of CNN's local feature extraction and transformer's global receptive field. This study invented a reliable, low-cost, and promising deep learning model for the automatic fine-grain classification of chicken Eimeria species, which could potentially be embedded in microscopic devices to improve the work efficiency of researchers and extended to other parasite ova, and applied to other agricultural tasks as a backbone.