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

Vogiatzis Oikonomidis, Ioannis; Cremona, Tiziana Patrizia; Lovric, Goran; Arcadu, Filippo; Stampanoni, Marco; Schittny, Johannes (2017). Effective segmentation of fresh post-mortem murine lung parenchyma in phase contrast X-ray tomographic microscopy images. Journal of Physics: Conference Series, 849(1), 012006. Institute of Physics Publishing IOP 10.1088/1742-6596/849/1/012006

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Pre-clinic Human Medicine > Institute of Anatomy
04 Faculty of Medicine > Pre-clinic Human Medicine > Institute of Anatomy > Topographical and Clinical Anatomy

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Vogiatzis Oikonomidis, Ioannis; Cremona, Tiziana Patrizia and Schittny, Johannes

Subjects:

500 Science > 570 Life sciences; biology
600 Technology > 610 Medicine & health

ISSN:

1742-6588

Publisher:

Institute of Physics Publishing IOP

Language:

English

Submitter:

Johannes Schittny

Date Deposited:

06 Dec 2017 14:59

Last Modified:

10 Dec 2017 02:23

Publisher DOI:

10.1088/1742-6596/849/1/012006

BORIS DOI:

10.7892/boris.107420

URI:

https://boris.unibe.ch/id/eprint/107420

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