title: Benchmark for multi-cellular segmentation of bright field microscopy images.
abstract: BACKGROUND
  Multi-cellular segmentation of bright field microscopy images is an essential computational step when quantifying collective migration of cells in vitro. Despite the availability of various tools and algorithms, no publicly available benchmark has been proposed for evaluation and comparison between the different alternatives.
  
  
  METHODS
  A uniform framework is presented to benchmark algorithms for multi-cellular segmentation in bright field microscopy images. A freely available set of 171 manually segmented images from diverse origins was partitioned into 8 datasets and evaluated on three leading designated tools.
  
  
  CONCLUSIONS
  The presented benchmark resource for evaluating segmentation algorithms of bright field images is the first public annotated dataset for this purpose. This annotated dataset of diverse examples allows fair evaluations and comparisons of future segmentation methods. Scientists are encouraged to assess new algorithms on this benchmark, and to contribute additional annotated datasets.
authors.affiliation: Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 69978, Israel. assafzar@gmail.com.
authors.forename: Assaf
authors.initials: A
authors.lastname: Zaritsky
authors.forename: Nathan
authors.initials: N
authors.lastname: Manor
authors.forename: Lior
authors.initials: L
authors.lastname: Wolf
authors.forename: Eshel
authors.initials: E
authors.lastname: Ben-Jacob
authors.forename: Ilan
authors.initials: I
authors.lastname: Tsarfaty
mesh_terms: D000465:Algorithms; D000818:Animals; D002465:Cell Movement / Q000502:physiology*; D003584:Cytological Techniques / Q000379:methods* / Q000592:standards; D004285:Dogs; D057809:HEK293 Cells; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods* / Q000592:standards; D061985:Madin Darby Canine Kidney Cells; D008853:Microscopy / Q000379:methods* / Q000592:standards