title: Normalization of multicolor fluorescence in situ hybridization (M-FISH) images for improving color karyotyping.
abstract: BACKGROUND
  Multiplex or multicolor fluorescence in situ hybridization (M-FISH) is a recently developed cytogenetic technique for cancer diagnosis and research on genetic disorders. By simultaneously viewing the multiply labeled specimens in different color channels, M-FISH facilitates the detection of subtle chromosomal aberrations. The success of this technique largely depends on the accuracy of pixel classification (color karyotyping). Improvements in classifier performance would allow the elucidation of more complex and more subtle chromosomal rearrangements. Normalization of M-FISH images has a significant effect on the accuracy of classification. In particular, misalignment or misregistration across multiple channels seriously affects classification accuracy. Image normalization, including automated registration, must be done before pixel classification.
  
  
  RESULTS
  We studied several image normalization approaches that affect image classification. In particular, we developed an automated registration technique to correct misalignment across the different fluor images (caused by chromatic aberration and other factors). This new registration algorithm is based on wavelets and spline approximations that have computational advantages and improved accuracy. To evaluate the performance improvement brought about by these data normalization approaches, we used the downstream pixel classification accuracy as a measurement. A Bayesian classifier assumed that each of 24 chromosome classes had a normal probability distribution. The effects that this registration and other normalization steps have on subsequent classification accuracy were evaluated on a comprehensive M-FISH database established by Advanced Digital Imaging Research (http://www.adires.com/05/Project/MFISH_DB/MFISH_DB.shtml).
  
  
  CONCLUSIONS
  Pixel misclassification errors result from different factors. These include uneven hybridization, spectral overlap among fluors, and image misregistration. Effective preprocessing of M-FISH images can decrease the effects of those factors and thereby increase pixel classification accuracy. The data normalization steps described in this report, such as image registration and background flattening, can significantly improve subsequent classification accuracy. An improved classifier in turn would allow subtle DNA rearrangements to be identified in genetic diagnosis and cancer research.
authors.affiliation: School of Computing and Engineering, University of Missouri, Kansas City, Missouri 64110, USA. wangyup@umkc.edu
authors.forename: Yu-Ping
authors.initials: YP
authors.lastname: Wang
authors.forename: Kenneth R
authors.initials: KR
authors.lastname: Castleman
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D002877:Chromosomes, Human / Q000737:chemistry / Q000235:genetics; D016208:Databases, Factual; D005456:Fluorescent Dyes / Q000737:chemistry; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D016018:Least-Squares Analysis; D008856:Microscopy, Fluorescence; D025341:Principal Component Analysis; D015203:Reproducibility of Results; D032681:Spectral Karyotyping / Q000379:methods*
chemical_list: D005456:Fluorescent Dyes