title: Fast segmentation of stained nuclei in terabyte-scale, time resolved 3D microscopy image stacks.
abstract: Automated analysis of multi-dimensional microscopy images has become an integral part of modern research in life science. Most available algorithms that provide sufficient segmentation quality, however, are infeasible for a large amount of data due to their high complexity. In this contribution we present a fast parallelized segmentation method that is especially suited for the extraction of stained nuclei from microscopy images, e.g., of developing zebrafish embryos. The idea is to transform the input image based on gradient and normal directions in the proximity of detected seed points such that it can be handled by straightforward global thresholding like Otsu's method. We evaluate the quality of the obtained segmentation results on a set of real and simulated benchmark images in 2D and 3D and show the algorithm's superior performance compared to other state-of-the-art algorithms. We achieve an up to ten-fold decrease in processing times, allowing us to process large data sets while still providing reasonable segmentation results.
authors.affiliation: Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Stegmaier
authors.affiliation: Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany.
authors.forename: Jens C
authors.initials: JC
authors.lastname: Otte
authors.affiliation: Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany ; Institute of Applied Physics (APH) and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology, Karlsruhe, Germany.
authors.forename: Andrei
authors.initials: A
authors.lastname: Kobitski
authors.affiliation: Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Bartschat
authors.affiliation: Steinbuch Center for Computing (SCC), Karlsruhe Institute of Technology, Karlsruhe, Germany.
authors.forename: Ariel
authors.initials: A
authors.lastname: Garcia
authors.affiliation: Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany ; Institute of Applied Physics (APH) and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology, Karlsruhe, Germany ; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America.
authors.forename: G Ulrich
authors.initials: GU
authors.lastname: Nienhaus
authors.affiliation: Institute for Toxicology and Genetics (ITG), Karlsruhe Institute of Technology, Karlsruhe, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Strähle
authors.affiliation: Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Karlsruhe, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Mikut
mesh_terms: D000465:Algorithms; D002467:Cell Nucleus; D007091:Image Processing, Computer-Assisted; D021621:Imaging, Three-Dimensional; D008853:Microscopy / Q000379:methods*; D008856:Microscopy, Fluorescence / Q000379:methods; D015203:Reproducibility of Results