title: A linear program formulation for the segmentation of Ciona membrane volumes.
abstract: We address the problem of cell segmentation in confocal microscopy membrane volumes of the ascidian Ciona used in the study of morphogenesis. The primary challenges are non-uniform and patchy membrane staining and faint spurious boundaries from other organelles (e.g. nuclei). Traditional segmentation methods incorrectly attach to faint boundaries producing spurious edges. To address this problem, we propose a linear optimization framework for the joint correction of multiple over-segmentations obtained from different methods. The main idea motivating this approach is that multiple over-segmentations, resulting from a pool of methods with various parameters, are likely to agree on the correct segment boundaries, while spurious boundaries are methodor parameter-dependent. The challenge is to make an optimized decision on selecting the correct boundaries while discarding the spurious ones. The proposed unsupervised method achieves better performance than state of the art methods for cell segmentation from membrane images.
authors: Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA 93106, USA.
authors: Diana L
authors: DL
authors: Delibaltov
authors: Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA 93106, USA.
authors: Pratim
authors: P
authors: Ghosh
authors: Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA 93106, USA.
authors: Volkan
authors: V
authors: Rodoplu
authors: Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
authors: Michael
authors: M
authors: Veeman
authors: Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
authors: William
authors: W
authors: Smith
authors: Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA 93106, USA.
authors: B S
authors: BS
authors: Manjunath
mesh_terms: D000465:Algorithms; D000818:Animals; D002462:Cell Membrane / Q000648:ultrastructure*; D002938:Ciona intestinalis / Q000166:cytology*; D007089:Image Enhancement / Q000379:methods; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D018613:Microscopy, Confocal / Q000379:methods*; D009929:Organ Size; D010363:Pattern Recognition, Automated / Q000379:methods*; D011382:Programming, Linear; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity