title: Antibiogramj: A tool for analysing images from disk diffusion tests.
abstract: OBJECTIVE
  Disk diffusion testing, known as antibiogram, is widely applied in microbiology to determine the antimicrobial susceptibility of microorganisms. The measurement of the diameter of the zone of growth inhibition of microorganisms around the antimicrobial disks in the antibiogram is frequently performed manually by specialists using a ruler. This is a time-consuming and error-prone task that might be simplified using automated or semi-automated inhibition zone readers. However, most readers are usually expensive instruments with embedded software that require significant changes in laboratory design and workflow.
  
  
  METHODS
  Based on the workflow employed by specialists to determine the antimicrobial susceptibility of microorganisms, we have designed a software tool that, from images of disk diffusion tests, semi-automatises the process. Standard computer vision techniques are employed to achieve such an automatisation.
  
  
  RESULTS
  We present AntibiogramJ, a user-friendly and open-source software tool to semi-automatically determine, measure and categorise inhibition zones of images from disk diffusion tests. AntibiogramJ is implemented in Java and deals with images captured with any device that incorporates a camera, including digital cameras and mobile phones. The fully automatic procedure of AntibiogramJ for measuring inhibition zones achieves an overall agreement of 87% with an expert microbiologist; moreover, AntibiogramJ includes features to easily detect when the automatic reading is not correct and fix it manually to obtain the correct result.
  
  
  CONCLUSIONS
  AntibiogramJ is a user-friendly, platform-independent, open-source, and free tool that, up to the best of our knowledge, is the most complete software tool for antibiogram analysis without requiring any investment in new equipment or changes in the laboratory.
authors.affiliation: Biochemistry and Molecular Biology Area, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain.
authors.forename: C A
authors.initials: CA
authors.lastname: Alonso
authors.affiliation: Department of Mathematics and Computer Science, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain.
authors.forename: C
authors.initials: C
authors.lastname: Domínguez
authors.affiliation: Department of Mathematics and Computer Science, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain. Electronic address: jonathan.heras@unirioja.es.
authors.forename: J
authors.initials: J
authors.lastname: Heras
authors.affiliation: Department of Mathematics and Computer Science, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain.
authors.forename: E
authors.initials: E
authors.lastname: Mata
authors.affiliation: Department of Mathematics and Computer Science, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain.
authors.forename: V
authors.initials: V
authors.lastname: Pascual
authors.affiliation: Biochemistry and Molecular Biology Area, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain.
authors.forename: C
authors.initials: C
authors.lastname: Torres
authors.affiliation: Biochemistry and Molecular Biology Area, University of La Rioja, Ed. Científico Tecnológico-CCT. C/ Madre de Dios, 53, Logroño, 26006, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Zarazaga
mesh_terms: D000150:Acinetobacter; D000900:Anti-Bacterial Agents / Q000737:chemistry*; D001331:Automation; D019295:Computational Biology; D004058:Diffusion; D001330:Electronic Data Processing; D004755:Enterobacteriaceae; D016983:Enterococcus; D008826:Microbial Sensitivity Tests; D011381:Programming Languages; D011549:Pseudomonas; D015203:Reproducibility of Results; D012984:Software; D013210:Staphylococcus; D014584:User-Computer Interface
chemical_list: D000900:Anti-Bacterial Agents
keywords: Antibiograms; Disk diffusion test; ImageJ; Inhibition zone reader; Learning system; OpenCV