title: Nonrigid registration of 3-d multichannel microscopy images of cell nuclei.
abstract: We present an intensity-based nonrigid registration approach for the normalization of 3-D multichannel microscopy images of cell nuclei. A main problem with cell nuclei images is that the intensity structure of different nuclei differs very much; thus, an intensity-based registration scheme cannot be used directly. Instead, we first perform a segmentation of the images from the cell nucleus channel, smooth the resulting images by a Gaussian filter, and then apply an intensity-based registration algorithm. The obtained transformation is applied to the images from the nucleus channel as well as to the images from the other channels. To improve the convergence rate of the algorithm, we propose an adaptive step length optimization scheme and also employ a multiresolution scheme. Our approach has been successfully applied using 2-D cell-like synthetic images, 3-D phantom images as well as 3-D multichannel microscopy images representing different chromosome territories and gene regions. We also describe an extension of our approach, which is applied for the registration of 3D + t (4-D) image series of moving cell nuclei.
authors.affiliation: Department of Bioinformatics and Functional Genomics, German Cancer Research Centre, University of Heidelberg, Heidelberg, Germany. s.yang@dkfz.de
authors.forename: S
authors.initials: S
authors.lastname: Yang
authors.forename: D
authors.initials: D
authors.lastname: Kohler
authors.forename: K
authors.initials: K
authors.lastname: Teller
authors.forename: T
authors.initials: T
authors.lastname: Cremer
authors.forename: P
authors.initials: P
authors.lastname: Le Baccon
authors.forename: E
authors.initials: E
authors.lastname: Heard
authors.forename: R
authors.initials: R
authors.lastname: Eils
authors.forename: K
authors.initials: K
authors.lastname: Rohr
mesh_terms: D000465:Algorithms; D002467:Cell Nucleus / Q000648:ultrastructure*; D007089:Image Enhancement / Q000379:methods*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008853:Microscopy / Q000379:methods*; D009716:Numerical Analysis, Computer-Assisted; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012815:Signal Processing, Computer-Assisted; D013382:Subtraction Technique