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Title: Quantitative Analysis Of Three-dimensional Branching Systems From X-ray Computed Microtomography Data

Abstract

Branching structures such as lungs, blood vessels and plant roots play a critical role in life. Growth, structure, and function of these branching structures have an immense effect on our lives. Therefore, quantitative size information on such structures in their native environment is invaluable for studying their growth and the effect of the environment on them. X-ray computed tomography (XCT) has been an effective tool for in situ imaging and analysis of branching structures. We developed a costless tool that approximates the surface and volume of branching structures. Our methodology of noninvasive imaging, segmentation and extraction of quantitative information is demonstrated through the analysis of a plant root in its soil medium from 3D tomography data. XCT data collected on a grass specimen was used to visualize its root structure. A suite of open-source software was employed to segment the root from the soil and determine its isosurface, which was used to calculate its volume and surface. This methodology of processing 3D data is applicable to other branching structures even when the structure of interest is of similar x-ray attenuation to its environment and difficulties arise with sample segmentation.

Authors:
;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1406816
Report Number(s):
PNNL-SA-120165
Journal ID: ISSN 1755-5191; 49216; KP1704020
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Imaging in Medicine; Journal Volume: 8; Journal Issue: 4
Country of Publication:
United States
Language:
English
Subject:
Environmental Molecular Sciences Laboratory

Citation Formats

McKinney, Adriana L., and Varga, Tamas. Quantitative Analysis Of Three-dimensional Branching Systems From X-ray Computed Microtomography Data. United States: N. p., 2016. Web.
McKinney, Adriana L., & Varga, Tamas. Quantitative Analysis Of Three-dimensional Branching Systems From X-ray Computed Microtomography Data. United States.
McKinney, Adriana L., and Varga, Tamas. Mon . "Quantitative Analysis Of Three-dimensional Branching Systems From X-ray Computed Microtomography Data". United States. doi:.
@article{osti_1406816,
title = {Quantitative Analysis Of Three-dimensional Branching Systems From X-ray Computed Microtomography Data},
author = {McKinney, Adriana L. and Varga, Tamas},
abstractNote = {Branching structures such as lungs, blood vessels and plant roots play a critical role in life. Growth, structure, and function of these branching structures have an immense effect on our lives. Therefore, quantitative size information on such structures in their native environment is invaluable for studying their growth and the effect of the environment on them. X-ray computed tomography (XCT) has been an effective tool for in situ imaging and analysis of branching structures. We developed a costless tool that approximates the surface and volume of branching structures. Our methodology of noninvasive imaging, segmentation and extraction of quantitative information is demonstrated through the analysis of a plant root in its soil medium from 3D tomography data. XCT data collected on a grass specimen was used to visualize its root structure. A suite of open-source software was employed to segment the root from the soil and determine its isosurface, which was used to calculate its volume and surface. This methodology of processing 3D data is applicable to other branching structures even when the structure of interest is of similar x-ray attenuation to its environment and difficulties arise with sample segmentation.},
doi = {},
journal = {Imaging in Medicine},
number = 4,
volume = 8,
place = {United States},
year = {Mon Aug 15 00:00:00 EDT 2016},
month = {Mon Aug 15 00:00:00 EDT 2016}
}