title: Superpixel-based segmentation of muscle fibers in multi-channel microscopy.
abstract: BACKGROUND
  Confetti fluorescence and other multi-color genetic labelling strategies are useful for observing stem cell regeneration and for other problems of cell lineage tracing. One difficulty of such strategies is segmenting the cell boundaries, which is a very different problem from segmenting color images from the real world. This paper addresses the difficulties and presents a superpixel-based framework for segmentation of regenerated muscle fibers in mice.
  
  
  RESULTS
  We propose to integrate an edge detector into a superpixel algorithm and customize the method for multi-channel images. The enhanced superpixel method outperforms the original and another advanced superpixel algorithm in terms of both boundary recall and under-segmentation error. Our framework was applied to cross-section and lateral section images of regenerated muscle fibers from confetti-fluorescent mice. Compared with "ground-truth" segmentations, our framework yielded median Dice similarity coefficients of 0.92 and higher.
  
  
  CONCLUSIONS
  Our segmentation framework is flexible and provides very good segmentations of multi-color muscle fibers. We anticipate our methods will be useful for segmenting a variety of tissues in confetti fluorecent mice and in mice with similar multi-color labels.
authors.affiliation: Centre for Computational Biology, and Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857, Singapore.|BioSystems and Micromechanics (BioSyM) Singapore - MIT Alliance for Research and Technology, Singapore, 138602, Singapore.
authors.forename: Binh P
authors.initials: BP
authors.lastname: Nguyen
authors.affiliation: Centre for Computational Biology, and Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857, Singapore.|BioSystems and Micromechanics (BioSyM) Singapore - MIT Alliance for Research and Technology, Singapore, 138602, Singapore.
authors.forename: Hans
authors.initials: H
authors.lastname: Heemskerk
authors.affiliation: BioSystems and Micromechanics (BioSyM) Singapore - MIT Alliance for Research and Technology, Singapore, 138602, Singapore.|Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
authors.forename: Peter T C
authors.initials: PT
authors.lastname: So
authors.affiliation: Centre for Computational Biology, and Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857, Singapore. lisa.tucker-kellogg@duke-nus.edu.sg.|BioSystems and Micromechanics (BioSyM) Singapore - MIT Alliance for Research and Technology, Singapore, 138602, Singapore. lisa.tucker-kellogg@duke-nus.edu.sg.
authors.forename: Lisa
authors.initials: L
authors.lastname: Tucker-Kellogg
mesh_terms: D000465:Algorithms; D002467:Cell Nucleus / Q000378:metabolism; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008853:Microscopy; D032342:Muscle Cells / Q000166:cytology*
keywords: Confetti fluorescence; Multi-channel microscopy; Muscle fibers; Segmentation; Superpixel