title: Automated image analysis of lung branching morphogenesis from microscopic images of fetal rat explants.
abstract: BACKGROUND
  Regulating mechanisms of branching morphogenesis of fetal lung rat explants have been an essential tool for molecular research. This work presents a new methodology to accurately quantify the epithelial, outer contour, and peripheral airway buds of lung explants during cellular development from microscopic images.
  
  
  METHODS
  The outer contour was defined using an adaptive and multiscale threshold algorithm whose level was automatically calculated based on an entropy maximization criterion. The inner lung epithelium was defined by a clustering procedure that groups small image regions according to the minimum description length principle and local statistical properties. Finally, the number of peripheral buds was counted as the skeleton branched ends from a skeletonized image of the lung inner epithelia.
  
  
  RESULTS
  The time for lung branching morphometric analysis was reduced in 98% in contrast to the manual method. Best results were obtained in the first two days of cellular development, with lesser standard deviations. Nonsignificant differences were found between the automatic and manual results in all culture days.
  
  
  CONCLUSIONS
  The proposed method introduces a series of advantages related to its intuitive use and accuracy, making the technique suitable to images with different lighting characteristics and allowing a reliable comparison between different researchers.
authors.affiliation: ICVS/3B's, PT Government Associate Laboratory, Guimarães, Braga, Portugal ; DIGARC, Polytechnic Institute of Cávado and Ave, Barcelos, Portugal ; Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal.
authors.forename: Pedro L
authors.initials: PL
authors.lastname: Rodrigues
authors.affiliation: ICVS/3B's, PT Government Associate Laboratory, Guimarães, Braga, Portugal ; DIGARC, Polytechnic Institute of Cávado and Ave, Barcelos, Portugal.
authors.forename: Nuno F
authors.initials: NF
authors.lastname: Rodrigues
authors.affiliation: DIGARC, Polytechnic Institute of Cávado and Ave, Barcelos, Portugal.
authors.forename: Duarte
authors.initials: D
authors.lastname: Duque
authors.affiliation: ICVS/3B's, PT Government Associate Laboratory, Guimarães, Braga, Portugal.
authors.forename: Sara
authors.initials: S
authors.lastname: Granja
authors.affiliation: ICVS/3B's, PT Government Associate Laboratory, Guimarães, Braga, Portugal.
authors.forename: Jorge
authors.initials: J
authors.lastname: Correia-Pinto
authors.affiliation: ICVS/3B's, PT Government Associate Laboratory, Guimarães, Braga, Portugal ; DIGARC, Polytechnic Institute of Cávado and Ave, Barcelos, Portugal.
authors.forename: João L
authors.initials: JL
authors.lastname: Vilaça
mesh_terms: D000465:Algorithms; D000818:Animals; D004848:Epithelium / Q000196:embryology*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D066298:In Vitro Techniques; D008168:Lung / Q000196:embryology*; D009024:Morphogenesis / Q000502:physiology*; D051381:Rats