title: An improved segmentation method for in vivo microCT imaging.
abstract: Image segmentation methods for microCT can influence the accuracy of bone morphometry calculations. A new automated segmentation method is introduced, and its performance is compared with standard segmentation methods. The new method can improve the results of in vivo microCT, where the need to keep radiation dose low limits scan quality.
  
  
  BACKGROUND
  An important topic for microCT analysis of bone samples is the segmentation of the original reconstructed grayscale data sets to separate bone from non-bone. Problems like noise, resolution limitations, and beam-hardening make this a nontrivial issue. Inappropriate segmentation methods will reduce the potential power of microCT and may introduce bias in the architectural measurements, in particular, when new in vivo microCT with its inherent limitations in scan quality is used. Here we introduce a new segmentation method using local thresholds and compare its performance to standard global segmentation methods.
  
  
  METHODS
  The local threshold method was validated by comparing the result of the segmentation with histology. Furthermore, the effect of choosing this new method versus standard segmentation methods using global threshold values was investigated by studying the sensitivity of these methods to signal to noise ratio and resolution.
  
  
  RESULTS
  Using the new method on high-quality scans yielded accurate results and virtually no differences between histology and the segmented data sets could be observed. When prior knowledge about the volume fraction of the bone was available the global threshold also resulted in appropriate results. Degrading the scan quality had only minor effects on the performance of the new segmentation method. Although global segmentation methods were not sensitive to noise, it was not possible to segment both lower mineralized thin trabeculae and the higher mineralized cortex correctly with the same threshold value.
  
  
  CONCLUSIONS
  At high resolutions, both the new local and conventional global segmentation methods gave near exact representations of the bone structure. When scanned samples are not homogenous (e.g., thick cortices and thin trabeculae) and when resolution is relatively low, the local segmentation method outperforms global methods. It maximizes the potential of in vivo microCT by giving good structural representation without the need to use longer scanning times that would increase absorption of harmful X-ray radiation by the living tissue.
authors.affiliation: Department of Orthopaedics, Erasmus Medical Centre, Rotterdam, The Netherlands.
authors.forename: Jan H
authors.initials: JH
authors.lastname: Waarsing
authors.forename: Judd S
authors.initials: JS
authors.lastname: Day
authors.forename: Harrie
authors.initials: H
authors.lastname: Weinans
mesh_terms: D000465:Algorithms; D000818:Animals; D001842:Bone and Bones / Q000000981:diagnostic imaging*; D007091:Image Processing, Computer-Assisted; D021621:Imaging, Three-Dimensional; D008852:Microradiography / Q000379:methods*; D051381:Rats; D015203:Reproducibility of Results; D014057:Tomography, X-Ray Computed / Q000379:methods*