title: OvaSpec - A vision-based instrument for assessing concentration and developmental stage of Trichuris suis parasite egg suspensions.
abstract: BACKGROUND
  OvaSpec is a new, fully automated, vision-based instrument for assessing the quantity (concentration) and quality (embryonation percentage) of Trichuris suis parasite eggs in liquid suspension. The eggs constitute the active pharmaceutical ingredient in a medicinal drug for the treatment of immune-mediated diseases such as Crohn׳s disease, ulcerative colitis, and multiple sclerosis.
  
  
  METHODS
  This paper describes the development of an automated microscopy technology, including methodological challenges and design decisions of relevance for the future development of comparable vision-based instruments. Morphological properties are used to distinguish eggs from impurities and two features of the egg contents under brightfield and darkfield illumination are used in a statistical classification to distinguish eggs with undifferentiated contents (non-embryonated eggs) from eggs with fully developed larvae inside (embryonated eggs).
  
  
  RESULTS
  For assessment of the instrument׳s performance, six egg suspensions of varying quality were used to generate a dataset of unseen images. Subsequently, annotation of the detected eggs and impurities revealed a high agreement with the manual, image-based assessments for both concentration and embryonation percentage (both error rates <1.0%). Similarly, a strong correlation was demonstrated in a final, blinded comparison with traditional microscopic assessments performed by an experienced laboratory technician.
  
  
  CONCLUSIONS
  The present study demonstrates the applicability of computer vision in the production, analysis, and quality control of T. suis eggs used as an active pharmaceutical ingredient for the treatment of autoimmune diseases.
authors.affiliation: Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark; Parasite Technologies A/S, Hørsholm, Denmark. Electronic address: jmb@life.ku.dk.
authors.forename: Johan Musaeus
authors.initials: JM
authors.lastname: Bruun
authors.affiliation: Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark.
authors.forename: Jens Michael
authors.initials: JM
authors.lastname: Carstensen
authors.affiliation: Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark.
authors.forename: Nermina
authors.initials: N
authors.lastname: Vejzagić
authors.affiliation: Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark.
authors.forename: Svend
authors.initials: S
authors.lastname: Christensen
authors.affiliation: Parasite Technologies A/S, Hørsholm, Denmark.
authors.forename: Allan
authors.initials: A
authors.lastname: Roepstorff
authors.affiliation: Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark; Parasite Technologies A/S, Hørsholm, Denmark. Electronic address: chk@plen.ku.dk.
authors.forename: Christian M O
authors.initials: CM
authors.lastname: Kapel
mesh_terms: D000818:Animals; D001688:Biological Products / Q000592:standards; D005243:Feces / Q000469:parasitology; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008018:Life Cycle Stages / Q000502:physiology; D008853:Microscopy / Q000379:methods*; D010274:Parasitology / Q000379:methods*; D013535:Suspensions; D013552:Swine; D013556:Swine, Miniature; D014258:Trichuris / Q000166:cytology*
chemical_list: D001688:Biological Products; D013535:Suspensions
keywords: Computer vision; Concentration; Darkfield microscopy; Embryonation percentage; Image analysis; Parasite egg classification; Trichuris suis eggs