title: IJ-OpenCV: Combining ImageJ and OpenCV for processing images in biomedicine.
abstract: The effective processing of biomedical images usually requires the interoperability of diverse software tools that have different aims but are complementary. The goal of this work is to develop a bridge to connect two of those tools: ImageJ, a program for image analysis in life sciences, and OpenCV, a computer vision and machine learning library.
  
  
  
  Based on a thorough analysis of ImageJ and OpenCV, we detected the features of these systems that could be enhanced, and developed a library to combine both tools, taking advantage of the strengths of each system. The library was implemented on top of the SciJava converter framework. We also provide a methodology to use this library.
  
  
  
  We have developed the publicly available library IJ-OpenCV that can be employed to create applications combining features from both ImageJ and OpenCV. From the perspective of ImageJ developers, they can use IJ-OpenCV to easily create plugins that use any functionality provided by the OpenCV library and explore different alternatives. From the perspective of OpenCV developers, this library provides a link to the ImageJ graphical user interface and all its features to handle regions of interest.
  
  
  
  The IJ-OpenCV library bridges the gap between ImageJ and OpenCV, allowing the connection and the cooperation of these two systems.
authors.affiliation: Department of Mathematics and Computer Science, University of La Rioja, Logroño, Spain.
authors.forename: César
authors.initials: C
authors.lastname: Domínguez
authors.affiliation: Department of Mathematics and Computer Science, University of La Rioja, Logroño, Spain. Electronic address: jonathan.heras@unirioja.es.
authors.forename: Jónathan
authors.initials: J
authors.lastname: Heras
authors.affiliation: Department of Mathematics and Computer Science, University of La Rioja, Logroño, Spain. Electronic address: vico.pascual@unirioja.es.
authors.forename: Vico
authors.initials: V
authors.lastname: Pascual
mesh_terms: D019295:Computational Biology / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D000069550:Machine Learning; D008490:Medical Informatics / Q000379:methods*; D008826:Microbial Sensitivity Tests; D012984:Software; D014584:User-Computer Interface
keywords: Biomedicine; Computer vision; Image processing; ImageJ; Interoperability; Machine learning; OpenCV