title: Airway tree segmentation in serial block-face cryomicrotome images of rat lungs.
abstract: A highly automated method for the segmentation of airways in the serial block-face cryomicrotome images of rat lungs is presented. First, a point inside of the trachea is manually specified. Then, a set of candidate airway centerline points is automatically identified. By utilizing a novel path extraction method, a centerline path between the root of the airway tree and each point in the set of candidate centerline points is obtained. Local disturbances are robustly handled by a novel path extraction approach, which avoids the shortcut problem of standard minimum cost path algorithms. The union of all centerline paths is utilized to generate an initial airway tree structure, and a pruning algorithm is applied to automatically remove erroneous subtrees or branches. Finally, a surface segmentation method is used to obtain the airway lumen. The method was validated on five image volumes of Sprague-Dawley rats. Based on an expert-generated independent standard, an assessment of airway identification and lumen segmentation performance was conducted. The average of airway detection sensitivity was 87.4% with a 95% confidence interval (CI) of (84.9, 88.6)%. A plot of sensitivity as a function of airway radius is provided. The combined estimate of airway detection specificity was 100% with a 95% CI of (99.4, 100)%. The average number and diameter of terminal airway branches was 1179 and 159 μm, respectively. Segmentation results include airways up to 31 generations. The regression intercept and slope of airway radius measurements derived from final segmentations were estimated to be 7.22 μm and 1.005, respectively. The developed approach enables the quantitative studies of physiology and lung diseases in rats, requiring detailed geometric airway models.
authors: Christian
authors: C
authors: Bauer
authors: Melissa A
authors: MA
authors: Krueger
authors: Wayne J
authors: WJ
authors: Lamm
authors: Brian J
authors: BJ
authors: Smith
authors: Robb W
authors: RW
authors: Glenny
authors: Reinhard R
authors: RR
authors: Beichel
mesh_terms: D000818:Animals; D015925:Cryopreservation / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008168:Lung / Q000033:anatomy & histology*; D008297:Male; D008867:Microtomy / Q000379:methods*; D019047:Phantoms, Imaging; D051381:Rats; D017207:Rats, Sprague-Dawley
references: Comput Med Imaging Graph. 2010 Oct;34(7):572-8
references: 20382502
references: J Appl Physiol (1985). 2012 Jun;112(11):1921-31
references: 22461437
references: IEEE Trans Med Imaging. 2000 Jun;19(6):568-76
references: 11026460
references: Proc Natl Acad Sci U S A. 1996 Feb 20;93(4):1591-5
references: 11607632
references: Am J Physiol Heart Circ Physiol. 2000 Nov;279(5):H2043-52
references: 11045936
references: Med Image Comput Comput Assist Interv. 2009;12(Pt 1):222-9
references: 20425991
references: Anat Rec (Hoboken). 2009 May;292(5):720-7
references: 19322825
references: IEEE Trans Image Process. 1998;7(3):359-69
references: 18276256
references: Med Image Anal. 2009 Dec;13(6):819-45
references: 19818675
references: Anat Rec (Hoboken). 2008 Aug;291(8):916-26
references: 18561195
references: J Appl Physiol (1985). 2010 May;108(5):1395-401
references: 20203067
references: Comput Med Imaging Graph. 2004 Jan-Mar;28(1-2):77-86
references: 15127752
references: IEEE Trans Med Imaging. 2010 Apr;29(4):982-97
references: 20335095
references: J Thorac Imaging. 2013 Sep;28(5):284-90
references: 23748651
references: IEEE Trans Pattern Anal Mach Intell. 2006 Jan;28(1):119-34
references: 16402624
references: Med Image Comput Comput Assist Interv. 2009;12(Pt 2):51-8
references: 20426095
references: J Physiol Pharmacol. 2009 Nov;60 Suppl 5:71-6
references: 20134043
references: Anat Rec (Hoboken). 2008 Dec;291(12):1628-48
references: 18951511
references: Respir Med. 2012 Dec;106(12):1655-64
references: 22974831