Eggs from the pig whipworm, Trichuris suis ova, constitute the active pharmaceutical ingredient in a drug candidate targeting immune-mediated diseases such as Crohn’s disease, multiple sclerosis, a.o. The drug candidate is currently being evaluated in clinical trials around the world. In the present PhD project, a microscopy-based vision instrument has been developed to automate the characterization of egg suspension quantity and quality. The instrument uses digital image analysis and statistical classification to detect and count the eggs and to characterize the developmental stages of the larvae inside the eggs based on morphology and darkfield scattering. The novel application of this technology is described in a patent application. The assessed concentration and embryonation percentage is used in the preparation of medicinal doses for the patients. The instrument has been evaluated against image annotations and manual microscopy on large sets of images from egg suspensions of varying quality. It shows low error rates and high agreement with manual microscopy with reduced variability and higher consistency. Furthermore, a proof of concept analysis was able to correlate early signs of degeneration of the larvae with the infectivity in minipigs, which is the current gold standard for measuring potency of the parasite eggs.