Automated Image Analysis for Detection of Coccidia in Poultry

Coccidiosis, caused by the protozoan Eimeria sp., is one of the most common and costly diseases impacting the poultry industry. To establish effective control measures, it is essential to identify these protozoa. Typical methods for identifying and determining the severity of the protozoal infection include intestinal lesion scoring or enumeration of the protozoal oocysts in fecal samples. Standard analysis methods require highly skilled technicians or veterinarians to manually identify and manually enumerate these protozoal parasites. This process is labor intensive, time-consuming, and susceptible to human error. None of the current methods available, including molecular flow cytometry or even digital image analysis, can determine if an oocyst is sporulated or not. Oocysts are not infectious until they sporulate. The goal of this study was to design an automated model using Artificial Intelligence (AI) to expedite the process of enumeration, improve the efficiency and accuracy of the species identification, and determine the ability of the oocysts to infect. To this end, we trained and evaluated computer vision models based on the Mask RCNN neural network architecture. A model was trained to detect and differentiate three species and to determine sporulation for each (totaling six detection groups). This model achieved a mean relative percentage difference (RPD) of 5.64%, representing a slight overcount compared to manual counts, averaging across all groups. The mean RPD for each group individually fell within a range from -33.37% to 52.72%. These results demonstrate that these models were speedy and had high agreement with manual counts, with minimal processing of field-quality samples. These models also could differentiate the sporulation status of the oocysts, providing critical diagnostic information for potential field applications.