Effective segmentation of fresh post-mortem murine lung parenchyma in phase contrast X-ray tomographic microscopy images

X-Ray Microscopy Conference 2016

Oikonomidis, Ioannis Vogiatzis^1,2 ; Cremona, Tiziana P.^1 ; Lovric, Goran^2,3 ; Arcadu, Filippo^2,4 ; Stampanoni, Marco^2,4 ; Schittny, Johannes C.^1

Institute of Anatomy, University of Bern, Bern

3012, Switzerland^1

Swiss Light Source, Paul Scherrer Institute, Villigen

5234, Switzerland^2

Center for Biomedical Imaging (CIBM), EPFL, Lausanne

1015, Switzerland^3

Institute for Biomedical Engineering, University and ETH Zurich, Zurich

8092, Switzerland^4

关键词: 3D segmentation;    Functional units;    Mammalian lungs;    Morphological analysis;    Multilevel filtering;    Phase contrasts;    Structural complexity;    X ray tomographic microscopies;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/849/1/012006/pdf
DOI  :  10.1088/1742-6596/849/1/012006

来源: IOP

【 摘 要 】

The acinus represents the functional unit of the mammalian lung. It is defined as the small tree of gas-exchanging airways, which is fed by the most distal purely conducting airway. Different hypotheses exist on how the fine structure of the acinus changes during ventilation and development. Since in classical 2-dimensional (2D) sections of the lung the borders of the acini are not detectable, every study of acini requires 3-dimensional (3D) datasets. As a basis for further studies of pulmonary acini we imaged rodent lungs as close to life as possible using phase contrast synchrotron radiation-based X-ray tomographic microscopy (SRXTM), and developed a protocol for the segmentation of the alveolar septa. The method is based on a combined multilevel filtering approach. Seeds are automatically defined for separate regions of tissue and airspace during each 2D filtering level and then given as input to a 3D random walk segmentation. Thus, the different types of artifacts present in the images are treated separately, taking into account the sample's structural complexity. The proposed procedure yields high-quality 3D segmentations of acinar microstructure that can be used for a reliable morphological analysis.