title: Three-dimensional vasculature reconstruction of tumour microenvironment via local clustering and classification.
abstract: The vasculature inside breast cancers is one important component of the tumour microenvironment. The investigation of its spatial morphology, distribution and interactions with cancer cells, including cancer stem cells, is essential for elucidating mechanisms of tumour development and treatment response. Using confocal microscopy and fluorescent markers, we have acquired three-dimensional images of vasculature within mammary tumours and normal mammary gland of mouse models. However, it is difficult to segment and reconstruct complex vasculature accurately from the in vivo three-dimensional images owing to the existence of uneven intensity and regions with low signal-to-noise ratios (SNR). To overcome these challenges, we have developed a novel three-dimensional vasculature segmentation method based on local clustering and classification. First, images of vasculature are clustered into local regions, whose boundaries well delineate vasculature even in low SNR and uneven intensity regions. Then local regions belonging to vasculature are identified by applying a semi-supervised classification method based on three informative features of the local regions. Comparison of results using simulated and real vasculature images, from mouse mammary tumours and normal mammary gland, shows that the new method outperforms existing methods, and can be used for three-dimensional images with uneven background and low SNR to achieve accurate vasculature reconstruction.
authors: Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute , Weill Cornell Medical College , Houston, TX 77030 , USA ; Department of Information Science, School of Mathematical Sciences and LMAM , Peking University , Beijing 100871 , People's Republic of China.
authors: Yanqiao
authors: Y
authors: Zhu
authors: Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute , Weill Cornell Medical College , Houston, TX 77030 , USA.
authors: Fuhai
authors: F
authors: Li
authors: Department of Molecular Physiology and Biophysics , Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030 , USA.
authors: Tegy J
authors: TJ
authors: Vadakkan
authors: Department of Developmental Biology , University of Pittsburgh , Pittsburgh, PA 15213 , USA.
authors: Mei
authors: M
authors: Zhang
authors: Department of Molecular Physiology and Biophysics , Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030 , USA ; Lester and Sue Smith Breast Center , Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030 , USA.
authors: John
authors: J
authors: Landua
authors: Department of Molecular and Cellular Biology , Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030 , USA ; Lester and Sue Smith Breast Center , Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030 , USA.
authors: Wei
authors: W
authors: Wei
authors: Department of Information Science, School of Mathematical Sciences and LMAM , Peking University , Beijing 100871 , People's Republic of China.
authors: Jinwen
authors: J
authors: Ma
authors: Department of Molecular Physiology and Biophysics , Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030 , USA.
authors: Mary E
authors: ME
authors: Dickinson
authors: Department of Molecular and Cellular Biology , Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030 , USA.
authors: Jeffrey M
authors: JM
authors: Rosen
authors: Department of Molecular and Cellular Biology , Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030 , USA ; Department of Radiology , Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030 , USA ; Lester and Sue Smith Breast Center , Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030 , USA.
authors: Michael T
authors: MT
authors: Lewis
authors: Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute , Weill Cornell Medical College , Houston, TX 77030 , USA.
authors: Ming
authors: M
authors: Zhan
authors: Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute , Weill Cornell Medical College , Houston, TX 77030 , USA ; Department of Molecular and Cellular Biology , Baylor College of Medicine , One Baylor Plaza, Houston, TX 77030 , USA.
authors: Stephen T C
authors: ST
authors: Wong
keywords: vasculature reconstruction, tumour microenvironment, vascular imaging