title: Objective threshold selection procedure (OTS) for segmentation of scanning laser confocal microscope images.
abstract: The determination of volumes and interface areas from confocal laser scanning microscopy (CLSM) images requires the identification of component objects by segmentation. An automated method for the determination of segmentation thresholds for CLSM imaging of biofilms was developed. The procedure, named objective threshold selection (OTS), is a three-dimensional development of the approach introduced by the popular robust automatic threshold selection (RATS) method. OTS is based on the statistical properties of local gray-values and gradients in the image. By characterizing the dependence between a volumetric feature and the intensity threshold used for image segmentation, the former can be determined with an arbitrary confidence level, with no need for user intervention. The identification of an objective segmentation procedure renders the possibility for the full automation of volume and interfacial area measurement. Images from two distinct biofilm systems, acquired using different experimental techniques and instrumental setups were segmented by OTS to determine biofilm volume and interfacial area. The reliability of measurements for each case was analyzed to identify optimal procedure for image acquisition. The automated OTS method was shown to reproduce values obtained manually by an experienced operator.
authors.affiliation: ITQB/UNL, R Qta Grande 6, 2780 Oeiras, Portugal.
authors.forename: J B
authors.initials: JB
authors.lastname: Xavier
authors.forename: A
authors.initials: A
authors.lastname: Schnell
authors.forename: S
authors.initials: S
authors.lastname: Wuertz
authors.forename: R
authors.initials: R
authors.lastname: Palmer
authors.forename: D C
authors.initials: DC
authors.lastname: White
authors.forename: J S
authors.initials: JS
authors.lastname: Almeida
mesh_terms: D001331:Automation / Q000295:instrumentation / Q000379:methods; D018441:Biofilms / Q000254:growth & development; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D018613:Microscopy, Confocal / Q000295:instrumentation* / Q000379:methods*; D010616:Phenanthrenes / Q000378:metabolism
chemical_list: D010616:Phenanthrenes; C031181:phenanthrene