title: PreMosa: extracting 2D surfaces from 3D microscopy mosaics.
abstract: BACKGROUND
  A significant focus of biological research is to understand the development, organization and function of tissues. A particularly productive area of study is on single layer epithelial tissues in which the adherence junctions of cells form a 2D manifold that is fluorescently labeled. Given the size of the tissue, a microscope must collect a mosaic of overlapping 3D stacks encompassing the stained surface. Downstream interpretation is greatly simplified by preprocessing such a dataset as follows: (i) extracting and mapping the stained manifold in each stack into a single 2D projection plane, (ii) correcting uneven illumination artifacts, (iii) stitching the mosaic planes into a single, large 2D image and (iv) adjusting the contrast.
  
  
  RESULTS
  We have developed PreMosa, an efficient, fully automatic pipeline to perform the four preprocessing tasks above resulting in a single 2D image of the stained manifold across which contrast is optimized and illumination is even. Notable features are as follows. First, the 2D projection step employs a specially developed algorithm that actually finds the manifold in the stack based on maximizing contrast, intensity and smoothness. Second, the projection step comes first, implying all subsequent tasks are more rapidly solved in 2D. And last, the mosaic melding employs an algorithm that globally adjusts contrasts amongst the 2D tiles so as to produce a seamless, high-contrast image. We conclude with an evaluation using ground-truth datasets and present results on datasets from Drosophila melanogaster wings and Schmidtae mediterranea ciliary components.
  
  
  METHODS
  PreMosa is available under https://cblasse.github.io/premosa.
  
  
  BACKGROUND
  blasse@mpi-cbg.de or myers@mpi-cbg.de.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.
authors.forename: Corinna
authors.initials: C
authors.lastname: Blasse
authors.affiliation: Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
authors.forename: Stephan
authors.initials: S
authors.lastname: Saalfeld
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.|Department of Neuroscience, Institut Pasteur, Paris 75015, France.
authors.forename: Raphaël
authors.initials: R
authors.lastname: Etournay
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.|The Francis Crick Institute, London NW1 1AT, UK.
authors.forename: Andreas
authors.initials: A
authors.lastname: Sagner
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Eaton
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.|Center for Systems Biology Dresden, Germany.
authors.forename: Eugene W
authors.initials: EW
authors.lastname: Myers
mesh_terms: D000465:Algorithms; D000818:Animals; D016477:Artifacts; D002923:Cilia / Q000648:ultrastructure; D004331:Drosophila melanogaster / Q000033:anatomy & histology; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008853:Microscopy / Q000379:methods*; D010986:Platyhelminths / Q000648:ultrastructure; D012984:Software; D014921:Wings, Animal / Q000033:anatomy & histology