title: Algorithms for improved 3-D reconstruction of live mammalian embryo vasculature from optical coherence tomography data.
abstract: BACKGROUND
  Robust reconstructions of the three-dimensional network of blood vessels in developing embryos imaged by optical coherence tomography (OCT) are needed for quantifying the longitudinal development of vascular networks in live mammalian embryos, in support of developmental cardiovascular research. Past computational methods [such as speckle variance (SV)] have demonstrated the feasibility of vascular reconstruction, but multiple challenges remain including: the presence of vessel structures at multiple spatial scales, thin blood vessels with weak flow, and artifacts resulting from bulk tissue motion (BTM).
  
  
  METHODS
  In order to overcome these challenges, this paper introduces a robust and scalable reconstruction algorithm based on a combination of anomaly detection algorithms and a parametric dictionary based sparse representation of blood vessels from structural OCT data.
  
  
  RESULTS
  Validation results using confocal data as the baseline demonstrate that the proposed method enables the detection of vessel segments that are either partially missed or weakly reconstructed using the SV method. Finally, quantitative measurements of vessel reconstruction quality indicate an overall higher quality of vessel reconstruction with the proposed method.
  
  
  CONCLUSIONS
  Results suggest that sparsity-integrated speckle anomaly detection (SSAD) is potentially a valuable tool for performing accurate quantification of the progression of vascular development in the mammalian embryonic yolk sac as imaged using OCT.
authors.affiliation: 1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Prathamesh M
authors.initials: PM
authors.lastname: Kulkarni
authors.affiliation: 1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Rey-Villamizar
authors.affiliation: 1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Amine
authors.initials: A
authors.lastname: Merouane
authors.affiliation: 1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Narendran
authors.initials: N
authors.lastname: Sudheendran
authors.affiliation: 1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Shang
authors.initials: S
authors.lastname: Wang
authors.affiliation: 1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Monica
authors.initials: M
authors.lastname: Garcia
authors.affiliation: 1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Irina V
authors.initials: IV
authors.lastname: Larina
authors.affiliation: 1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Badrinath
authors.initials: B
authors.lastname: Roysam
authors.affiliation: 1 Department of Electrical and Computer Engineering, 2 Department of Biomedical Engineering, University of Houston, Houston, TX, USA ; 3 Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Kirill V
authors.initials: KV
authors.lastname: Larin
keywords: 3-D vessel reconstruction; Optical coherence tomography (OCT); live imaging